From 526be3e253ad9c4e10b619000331e9eceb5e0d26 Mon Sep 17 00:00:00 2001
From: Juan <juannicolash01@gmail.com>
Date: Fri, 1 Aug 2025 13:24:22 -0300
Subject: [PATCH 01/47] Base front end page

---
 src/frontend/static/frontend/rspack.common.js |  1 +
 .../frontend/src/components/MainNavbar.tsx    | 11 +++-
 .../DifferentialExpressionForm.tsx            | 56 +++++++++++++++++++
 .../DifferentialExpressionPanel.tsx           | 11 ++++
 .../src/css/differential-expression.css       |  0
 .../frontend/src/differential-expression.tsx  |  8 +++
 src/frontend/templates/frontend/base.html     |  1 +
 .../frontend/differential-expression.html     | 20 +++++++
 src/frontend/urls.py                          |  4 +-
 src/frontend/views.py                         | 10 ++++
 10 files changed, 120 insertions(+), 2 deletions(-)
 create mode 100644 src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
 create mode 100644 src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
 create mode 100644 src/frontend/static/frontend/src/css/differential-expression.css
 create mode 100644 src/frontend/static/frontend/src/differential-expression.tsx
 create mode 100644 src/frontend/templates/frontend/differential-expression.html

diff --git a/src/frontend/static/frontend/rspack.common.js b/src/frontend/static/frontend/rspack.common.js
index df78ea52..e7f41f91 100644
--- a/src/frontend/static/frontend/rspack.common.js
+++ b/src/frontend/static/frontend/rspack.common.js
@@ -14,6 +14,7 @@ const PATHS = {
 
 export const common = {
     entry: {
+        differentialExpression: `${PATHS.src}/differential-expression.tsx`,
         base: `${PATHS.src}/base.tsx`,
         gem: `${PATHS.src}/gem.tsx`,
         main: `${PATHS.src}/index.tsx`,
diff --git a/src/frontend/static/frontend/src/components/MainNavbar.tsx b/src/frontend/static/frontend/src/components/MainNavbar.tsx
index 060d3d21..ba2a96f5 100644
--- a/src/frontend/static/frontend/src/components/MainNavbar.tsx
+++ b/src/frontend/static/frontend/src/components/MainNavbar.tsx
@@ -17,6 +17,7 @@ declare const urlInstitutions: string
 declare const urlCGDSPanel: string
 declare const urlAboutUs: string
 declare const urlOpenSource: string
+declare const urlDifferentialExpression: string
 
 /** Component's Props */
 interface LogInLogOutPanelProps {
@@ -149,7 +150,7 @@ const LogInLogOutPanel = (props: LogInLogOutPanelProps) => {
     )
 }
 
-type ActiveItemOptions = 'home' | 'pipeline' | 'files' | 'cgds' | 'survival' | 'institutions' | 'about-us' | 'biomarkers' | 'open-source'
+type ActiveItemOptions = 'home' | 'pipeline' | 'files' | 'cgds' | 'survival' | 'institutions' | 'about-us' | 'biomarkers' | 'open-source' | 'differential-expression'
 
 interface MainNavbarProps {
     activeItem?: ActiveItemOptions,
@@ -230,6 +231,14 @@ const MainNavbar = (props: MainNavbarProps) => {
                                     as='a' href={urlBiomarkers}
                                     active={props.activeItem === 'biomarkers'}
                                 />
+
+                                {/* Differential Expression panel */}
+                                <Dropdown.Item
+                                    text='Differential expression'
+                                    icon='list layout'
+                                    as='a' href={urlDifferentialExpression}
+                                    active={props.activeItem === 'differential-expression'}
+                                />
                             </Dropdown.Menu>
                         </Dropdown>
                     </Menu.Menu>
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
new file mode 100644
index 00000000..b50f5638
--- /dev/null
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
@@ -0,0 +1,56 @@
+import React from 'react'
+import { Input, TextArea } from 'semantic-ui-react'
+import { SourceForm } from '../pipeline/SourceForm'
+
+export const DifferentialExpressionForm = () => {
+    return (
+        <div>
+            <Input placeholder='Search...' />
+            <TextArea placeholder='Tell us more' />
+            {/* mRNA SourceForm */}
+           {/*  <SourceForm
+                source={newExperiment.mRNASource}
+                headerTitle='mRNA profile'
+                headerIcon={{
+                    type: 'img',
+                    src: 'static/frontend/img/profiles/mRNA.svg'
+                }}
+                fileType={FileType.MRNA}
+                disabled={isEditing}
+                tagOptions={this.props.tagOptions}
+                handleChangeSourceType={(selectedSourceType) => {
+                    this.props.handleChangeSourceType(selectedSourceType, 'mRNASource')
+                }}
+                selectNewFile={this.props.selectNewFile}
+                selectUploadedFile={(selectedFile) => {
+                    this.props.selectUploadedFile(selectedFile, 'mRNASource')
+                }}
+                selectStudy={(selectedStudy) => {
+                    this.props.selectStudy(selectedStudy, 'mRNASource')
+                }}
+            /> */}
+            {/* Clinical SourceForm */}
+           {/*  <SourceForm
+                source={newExperiment.mRNASource}
+                headerTitle='mRNA profile'
+                headerIcon={{
+                    type: 'img',
+                    src: 'static/frontend/img/profiles/mRNA.svg'
+                }}
+                fileType={FileType.MRNA}
+                disabled={isEditing}
+                tagOptions={this.props.tagOptions}
+                handleChangeSourceType={(selectedSourceType) => {
+                    this.props.handleChangeSourceType(selectedSourceType, 'mRNASource')
+                }}
+                selectNewFile={this.props.selectNewFile}
+                selectUploadedFile={(selectedFile) => {
+                    this.props.selectUploadedFile(selectedFile, 'mRNASource')
+                }}
+                selectStudy={(selectedStudy) => {
+                    this.props.selectStudy(selectedStudy, 'mRNASource')
+                }}
+            /> */}
+        </div>
+    )
+}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
new file mode 100644
index 00000000..33611d89
--- /dev/null
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -0,0 +1,11 @@
+import React from 'react'
+import { Base } from '../Base'
+import { DifferentialExpressionForm } from './DifferentialExpressionForm'
+
+export const DiferentialExpressionPanel = () => {
+    return (
+        <Base activeItem='differential-expression' wrapperClass='wrapper'>
+            <DifferentialExpressionForm />
+        </Base>
+    )
+}
diff --git a/src/frontend/static/frontend/src/css/differential-expression.css b/src/frontend/static/frontend/src/css/differential-expression.css
new file mode 100644
index 00000000..e69de29b
diff --git a/src/frontend/static/frontend/src/differential-expression.tsx b/src/frontend/static/frontend/src/differential-expression.tsx
new file mode 100644
index 00000000..e7f2be87
--- /dev/null
+++ b/src/frontend/static/frontend/src/differential-expression.tsx
@@ -0,0 +1,8 @@
+import React from 'react'
+import { createRoot } from 'react-dom/client'
+import './css/differential-expression.css'
+import { DiferentialExpressionPanel } from './components/differential-expression/DifferentialExpressionPanel'
+
+const container = document.getElementById('differential-expression-app')
+const root = createRoot(container!)
+root.render(<DiferentialExpressionPanel />)
diff --git a/src/frontend/templates/frontend/base.html b/src/frontend/templates/frontend/base.html
index 4d7a9fbc..6b4e0393 100644
--- a/src/frontend/templates/frontend/base.html
+++ b/src/frontend/templates/frontend/base.html
@@ -54,6 +54,7 @@
         const urlSurvival = "{% url 'survival' %}" {# URL to the Survival Analysis Panel #}
         const urlBiomarkers = "{% url 'biomarkers' %}" {# URL to the Biomarkers Panel #}
         const urlAboutUs = "{% url 'about_us' %}" {# URL to About us page #}
+        const urlDifferentialExpression = "{% url 'differential_expression' %}" {# URL to About us page #}
         const urlOpenSource = "{% url 'open_source' %}" {# URL to About us page #}
         const urlClinicalSourceUserFileCRUD = "{% url 'clinical_source_user_file' %}"
         const urlSearchUser = "{% url 'search_user' %}" {# URL to search user view #}
diff --git a/src/frontend/templates/frontend/differential-expression.html b/src/frontend/templates/frontend/differential-expression.html
new file mode 100644
index 00000000..0065ea46
--- /dev/null
+++ b/src/frontend/templates/frontend/differential-expression.html
@@ -0,0 +1,20 @@
+{% extends 'frontend/base.html' %}
+{% load static %}
+{% load render_bundle from webpack_loader %}
+
+{% block title %}| Differential expression experiments{% endblock %}
+{% block meta_description %}Todo: cambiar Description.{% endblock %}
+
+{% block css %}
+        {% render_bundle 'differentialExpression' 'css' %}
+{% endblock %}
+
+{% block content %}
+        <main id="differential-expression-app"></main>
+{% endblock %}
+
+{% block js %}
+        <script>
+        </script>
+        {% render_bundle 'differentialExpression' 'js' %}
+{% endblock %}
\ No newline at end of file
diff --git a/src/frontend/urls.py b/src/frontend/urls.py
index dd05e672..eefe99a1 100644
--- a/src/frontend/urls.py
+++ b/src/frontend/urls.py
@@ -8,6 +8,8 @@
     path('survival', views.survival_action, name='survival'),
     path('about-us', views.about_us_action, name='about_us'),
     path('open-source', views.open_source, name='open_source'),
-    path('site-policy', views.terms_and_privacy_policy_action, name='site_policy')
+    path('site-policy', views.terms_and_privacy_policy_action, name='site_policy'),
+    path('biomarker', views.biomarker, name='biomarker'),
+    path('differential-expression', views.differential_expression, name='differential_expression')
 ]
 
diff --git a/src/frontend/views.py b/src/frontend/views.py
index dac426ec..3a402345 100644
--- a/src/frontend/views.py
+++ b/src/frontend/views.py
@@ -42,6 +42,16 @@ def survival_action(request):
     """Survival Analysis view"""
     return render(request, "frontend/survival.html")
 
+@login_required
+def biomarker(request):
+    """Biomarker view"""
+    return render(request, "frontend/biomarker.html")
+
+@login_required
+def differential_expression(request):
+    """Differential expression experiment view"""
+    return render(request, "frontend/differential-expression.html")
+
 
 def open_source(request):
     """Open source view"""

From 07ddcffc48d83838959143e507995094cb6bacc9 Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Sun, 3 Aug 2025 16:42:16 -0300
Subject: [PATCH 02/47] Add differential expression experiment model and API

Introduces the DifferentialExpressionExperiment model, serializer, and API endpoints for listing and submitting experiments. Adds initial migration, model definition, serializer, and views for experiment management. Integrates the new app's URLs into the main project routing.
---
 .../migrations/0001_initial.py                |  37 ++++++
 src/differential_expression/models.py         |  50 ++++++++
 src/differential_expression/serializers.py    |  22 ++++
 src/differential_expression/urls.py           |   7 ++
 src/differential_expression/views.py          | 111 ++++++++++++++++++
 src/multiomics_intermediate/urls.py           |   1 +
 6 files changed, 228 insertions(+)
 create mode 100644 src/differential_expression/migrations/0001_initial.py
 create mode 100644 src/differential_expression/serializers.py
 create mode 100644 src/differential_expression/urls.py

diff --git a/src/differential_expression/migrations/0001_initial.py b/src/differential_expression/migrations/0001_initial.py
new file mode 100644
index 00000000..6910afbc
--- /dev/null
+++ b/src/differential_expression/migrations/0001_initial.py
@@ -0,0 +1,37 @@
+# Generated by Django 4.2.19 on 2025-08-03 19:37
+
+from django.conf import settings
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('institutions', '0005_alter_institution_options_and_more'),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('api_service', '0061_alter_experiment_shared_users'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='DifferentialExpressionExperiment',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=300)),
+                ('description', models.TextField(blank=True, null=True)),
+                ('clinical_attribute', models.CharField(max_length=100)),
+                ('threshold_percentile', models.FloatField(default=0.15)),
+                ('threshold', models.FloatField(default=0.0001)),
+                ('task_id', models.CharField(blank=True, max_length=100, null=True)),
+                ('is_public', models.BooleanField(default=False)),
+                ('clinical_source', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='differential_expression_as_clinical', to='api_service.experimentclinicalsource')),
+                ('mrna_source', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='differential_expression_as_mrna', to='api_service.experimentsource')),
+                ('shared_institutions', models.ManyToManyField(blank=True, related_name='shared_differential_expression', to='institutions.institution')),
+                ('shared_users', models.ManyToManyField(blank=True, related_name='shared_users_differential_expression', to=settings.AUTH_USER_MODEL)),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+            ],
+        ),
+    ]
diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index 5482a0c3..5235d1e2 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -1 +1,51 @@
 from django.db import models
+from django.contrib.auth import get_user_model
+from institutions.models import Institution
+from django.contrib.auth.models import User
+
+
+class DifferentialExpressionExperiment(models.Model):
+    """
+    Model to create and manage differential expression data.
+    """
+
+    name = models.CharField(max_length=300)
+    description = models.TextField(blank=True, null=True)
+
+    # Sources
+    clinical_source = models.ForeignKey('api_service.ExperimentClinicalSource', on_delete=models.CASCADE, null=False,
+                                        blank=False, related_name='differential_expression_as_clinical')
+
+    mrna_source = models.ForeignKey('api_service.ExperimentSource', on_delete=models.CASCADE, null=False, blank=False,
+                                    related_name='differential_expression_as_mrna')
+
+    clinical_attribute = models.CharField(max_length=100, blank=False, null=False)
+
+    threshold_percentile = models.FloatField(default=0.15, blank=False, null=False)
+
+    threshold = models.FloatField(default=0.0001, blank=False, null=False)
+
+    task_id = models.CharField(max_length=100, blank=True, null=True)
+
+    user = models.ForeignKey(get_user_model(), on_delete=models.CASCADE)
+    is_public = models.BooleanField(blank=False, null=False, default=False)
+    shared_institutions = models.ManyToManyField(Institution, related_name='shared_differential_expression', blank=True)
+    shared_users = models.ManyToManyField(User, blank=True,
+                                          related_name='shared_users_differential_expression')
+
+    def __str__(self):
+        return f"Differential Expression Experiment: {self.name}"
+
+    def save(self, *args, **kwargs):
+        """
+        Override the save method to ensure that the name is unique.
+        """
+        if not self.name:
+            raise ValueError("Experiment name cannot be empty.")
+
+        # # Ensure the name is unique
+        # if DifferentialExpressionExperiment.objects.filter(name=self.name).exists():
+        #     raise ValueError(f"An experiment with the name '{self.name}' already exists.")
+
+        super().save(*args, **kwargs)
+        
\ No newline at end of file
diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
new file mode 100644
index 00000000..7ec6fb13
--- /dev/null
+++ b/src/differential_expression/serializers.py
@@ -0,0 +1,22 @@
+from rest_framework import serializers
+
+from differential_expression.models import DifferentialExpressionExperiment
+from drf_writable_nested import WritableNestedModelSerializer
+
+
+class DifferentialExpressionExperimentSerializer(WritableNestedModelSerializer):
+    """
+    Serializer for Differential Expression Experiment.
+    """
+    id = serializers.IntegerField(read_only=True)
+    name = serializers.CharField(max_length=255)
+    description = serializers.CharField(allow_blank=True, required=False)
+    user = serializers.HiddenField(
+        default=serializers.CurrentUserDefault()
+    )
+    clinical_source = serializers.CharField(max_length=255, required=False)
+    mrna_source = serializers.CharField(max_length=255, required=False)
+
+    class Meta:
+        model = DifferentialExpressionExperiment
+        fields = '__all__'
\ No newline at end of file
diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
new file mode 100644
index 00000000..ba54be6c
--- /dev/null
+++ b/src/differential_expression/urls.py
@@ -0,0 +1,7 @@
+from django.urls import path
+from . import views
+
+urlpatterns = [
+    path('', views.DifferentialExpressionList.as_view(), name='differential_expression_list'),
+    path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
+]
\ No newline at end of file
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 200df7ba..498f680b 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -1 +1,112 @@
 from django.shortcuts import render
+from django.db import transaction
+from rest_framework.request import Request
+from rest_framework.views import APIView
+from common.utils import get_source_pk
+from api_service.utils import get_experiment_source
+from user_files.models_choices import FileType
+from rest_framework.exceptions import ValidationError
+from differential_expression.models import DifferentialExpressionExperiment
+from rest_framework.response import Response
+from rest_framework import generics, permissions, filters, status
+from rest_framework.generics import get_object_or_404
+from django.db.models import QuerySet, Q
+from differential_expression.serializers import DifferentialExpressionExperimentSerializer
+from django_filters.rest_framework import DjangoFilterBackend
+from common.pagination import StandardResultsSetPagination
+
+class DifferentialExpressionList(generics.ListAPIView):
+    """
+    Endpoint to list all differential expression experiments.
+    """
+
+    def get_queryset(self):
+        """
+        Endpoint to list all differential expression experiments.
+        """
+        user = self.request.user
+        experiments = DifferentialExpressionExperiment.objects.filter(
+            # Q(is_public=True) |
+            Q(user=user) |
+            Q(shared_institutions__institutionadministration__user=user) |
+            Q(shared_users=user)
+        ).distinct()
+
+
+        return experiments
+
+    serializer_class = DifferentialExpressionExperimentSerializer
+    permission_classes = [permissions.IsAuthenticated]
+    pagination_class = StandardResultsSetPagination
+    filter_backends = [filters.OrderingFilter, filters.SearchFilter, DjangoFilterBackend]
+
+
+class DifferentialExpressionSubmit(APIView):
+    """
+    Endpoint to submit a differential expression experiment.
+    """
+
+    def post(self, request : Request):
+        """
+        Endpoint to submit a differential expression experiment.
+        """
+        with transaction.atomic():
+
+            name = request.POST.get('name', 'Differential Expression Experiment')
+            description = request.POST.get('description', '')
+
+            # Clinical source
+            clinical_source_type = get_source_pk(request.POST, 'clinicalType')
+            clinical_source, clinical_aux = get_experiment_source(clinical_source_type, request, FileType.CLINICAL,
+                                                                  'clinical')
+
+            # Select the valid one (if it's a CGDSStudy it needs clinical_aux as it has both needed CGDSDatasets)
+            clinical_source = clinical_aux if clinical_aux is not None else clinical_source
+
+            if clinical_source is None:
+                raise ValidationError('Invalid clinical source')
+
+            # mRNA source
+            mrna_source_type = get_source_pk(request.POST, 'mRNAType')
+            mrna_source, _mrna_clinical = get_experiment_source(mrna_source_type, request, FileType.MRNA, 'mRNA')
+
+            if mrna_source is None:
+                raise ValidationError('Invalid mRNA source')
+
+            # Clinical attribute
+            clinical_attribute = request.POST.get('clinicalAttribute', None)
+            if not clinical_attribute:
+                raise ValidationError('Clinical attribute is required')
+
+            # Threshold percentile
+            try:
+                threshold_percentile = float(request.POST.get('thresholdPercentile', 0.15))
+            except ValueError:
+                raise ValidationError('Invalid threshold percentile value')
+
+            if threshold_percentile < 0 or threshold_percentile > 1:
+                raise ValidationError('Threshold percentile must be between 0 and 1')
+
+            # Threshold
+            try:
+                threshold = float(request.POST.get('threshold', 0.0001))
+            except ValueError:
+                raise ValidationError('Invalid threshold value')
+
+            if threshold < 0 or threshold > 1:
+                raise ValidationError('Threshold must be between 0 and 1')
+
+
+            # Create the differential expression experiment
+            experiment = DifferentialExpressionExperiment.objects.create(
+                name=name,
+                description=description,
+                clinical_source=clinical_source,
+                mrna_source=mrna_source,
+                clinical_attribute=clinical_attribute,
+                threshold_percentile=threshold_percentile,
+                threshold=threshold,
+                user = request.user,
+            )
+
+            return Response({'ok': True})
diff --git a/src/multiomics_intermediate/urls.py b/src/multiomics_intermediate/urls.py
index e5029a6b..436b0a95 100644
--- a/src/multiomics_intermediate/urls.py
+++ b/src/multiomics_intermediate/urls.py
@@ -32,6 +32,7 @@
     path('biomarkers/', include('biomarkers.urls')),
     path('statistical-props/', include('statistical_properties.urls')),
     path('feature-selection/', include('feature_selection.urls')),
+    path('differential-expression/', include('differential_expression.urls')),
     path('inference/', include('inferences.urls')),
     path('molecules/', include('molecules_details.urls')),
     path('admin/', admin.site.urls),

From 42ff66592627b1b1ba95857961bc9d2f98b26463 Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Thu, 7 Aug 2025 22:31:46 -0300
Subject: [PATCH 03/47] Add differential expression service, tasks, and
 migrations

Introduces new service and task modules for differential expression, adds related Django migrations, and updates models, views, and URLs to support new experiment features. Also adds a regression example notebook and updates feature selection tasks.
---
 ...alexpressionexperiment_attempt_and_more.py |  59 ++++
 ..._differentialexpressionexperiment_state.py |  37 +++
 src/differential_expression/models.py         |  33 +-
 src/differential_expression/service.py        | 290 ++++++++++++++++++
 src/differential_expression/tasks.py          |  79 +++++
 src/differential_expression/urls.py           |   1 +
 src/differential_expression/views.py          |  45 ++-
 src/feature_selection/tasks.py                |   2 +-
 8 files changed, 541 insertions(+), 5 deletions(-)
 create mode 100644 src/differential_expression/migrations/0002_differentialexpressionexperiment_attempt_and_more.py
 create mode 100644 src/differential_expression/migrations/0003_alter_differentialexpressionexperiment_state.py
 create mode 100644 src/differential_expression/service.py
 create mode 100644 src/differential_expression/tasks.py

diff --git a/src/differential_expression/migrations/0002_differentialexpressionexperiment_attempt_and_more.py b/src/differential_expression/migrations/0002_differentialexpressionexperiment_attempt_and_more.py
new file mode 100644
index 00000000..f7429abb
--- /dev/null
+++ b/src/differential_expression/migrations/0002_differentialexpressionexperiment_attempt_and_more.py
@@ -0,0 +1,59 @@
+# Generated by Django 4.2.19 on 2025-08-05 01:30
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("differential_expression", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="differentialexpressionexperiment",
+            name="attempt",
+            field=models.PositiveSmallIntegerField(
+                default=0,
+                help_text="Number of attempts to prevent a buggy experiment running forever",
+            ),
+        ),
+        migrations.AddField(
+            model_name="differentialexpressionexperiment",
+            name="execution_time",
+            field=models.FloatField(
+                blank=True,
+                default=0.0,
+                help_text="Execution time in seconds",
+                null=True,
+            ),
+        ),
+        migrations.AddField(
+            model_name="differentialexpressionexperiment",
+            name="state",
+            field=models.IntegerField(
+                choices=[
+                    (1, "Completed"),
+                    (2, "Finished With Error"),
+                    (3, "In Process"),
+                    (4, "Waiting For Queue"),
+                    (5, "No Samples In Common"),
+                    (6, "Stopping"),
+                    (7, "Stopped"),
+                    (8, "Reached Attempts Limit"),
+                    (9, "No Features Found"),
+                    (10, "Empty Dataset"),
+                    (11, "Timeout Exceeded"),
+                ],
+                default=4,
+                help_text="State of the differential expression experiment",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="differentialexpressionexperiment",
+            name="task_id",
+            field=models.CharField(
+                blank=True, help_text="Celery Task ID", max_length=100, null=True
+            ),
+        ),
+    ]
diff --git a/src/differential_expression/migrations/0003_alter_differentialexpressionexperiment_state.py b/src/differential_expression/migrations/0003_alter_differentialexpressionexperiment_state.py
new file mode 100644
index 00000000..f24d56c1
--- /dev/null
+++ b/src/differential_expression/migrations/0003_alter_differentialexpressionexperiment_state.py
@@ -0,0 +1,37 @@
+# Generated by Django 4.2.19 on 2025-08-05 01:43
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "differential_expression",
+            "0002_differentialexpressionexperiment_attempt_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="differentialexpressionexperiment",
+            name="state",
+            field=models.IntegerField(
+                choices=[
+                    (1, "Completed"),
+                    (2, "Finished With Error"),
+                    (3, "In Process"),
+                    (4, "Waiting For Queue"),
+                    (5, "No Samples In Common"),
+                    (6, "Stopping"),
+                    (7, "Stopped"),
+                    (8, "Reached Attempts Limit"),
+                    (9, "No Features Found"),
+                    (10, "Empty Dataset"),
+                    (11, "Timeout Exceeded"),
+                ],
+                default=4,
+                help_text="Current state of the differential expression experiment",
+            ),
+        ),
+    ]
diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index 5235d1e2..e70e911e 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -4,6 +4,20 @@
 from django.contrib.auth.models import User
 
 
+class DifferentialExpressionExperimentState(models.IntegerChoices):
+    """All the possible states of a Differential Expression Experiment."""
+    COMPLETED = 1
+    FINISHED_WITH_ERROR = 2
+    IN_PROCESS = 3
+    WAITING_FOR_QUEUE = 4
+    NO_SAMPLES_IN_COMMON = 5
+    STOPPING = 6
+    STOPPED = 7
+    REACHED_ATTEMPTS_LIMIT = 8
+    NO_FEATURES_FOUND = 9
+    EMPTY_DATASET = 10
+    TIMEOUT_EXCEEDED = 11
+
 class DifferentialExpressionExperiment(models.Model):
     """
     Model to create and manage differential expression data.
@@ -12,7 +26,8 @@ class DifferentialExpressionExperiment(models.Model):
     name = models.CharField(max_length=300)
     description = models.TextField(blank=True, null=True)
 
-    # Sources
+    # Clinical and mRNA sources
+    # These are used to link the experiment to the clinical and mRNA data sources
     clinical_source = models.ForeignKey('api_service.ExperimentClinicalSource', on_delete=models.CASCADE, null=False,
                                         blank=False, related_name='differential_expression_as_clinical')
 
@@ -25,8 +40,20 @@ class DifferentialExpressionExperiment(models.Model):
 
     threshold = models.FloatField(default=0.0001, blank=False, null=False)
 
-    task_id = models.CharField(max_length=100, blank=True, null=True)
-
+    # Celery task related fields
+    # This is used to track the execution of the task and its state
+    execution_time = models.FloatField(default=0.0, blank=True, null=True, help_text='Execution time in seconds')
+    task_id = models.CharField(max_length=100, blank=True, null=True, help_text='Celery Task ID')
+    attempt = models.PositiveSmallIntegerField(default=0, help_text='Number of attempts to prevent a buggy experiment '
+                                                                    'running forever')
+    state : int = models.IntegerField(
+        choices=DifferentialExpressionExperimentState.choices,
+        default=DifferentialExpressionExperimentState.WAITING_FOR_QUEUE,
+        help_text='Current state of the differential expression experiment'
+    )
+    
+    # User and sharing information
+    # This is used to track the user who created the experiment and to share it with other users or institutions
     user = models.ForeignKey(get_user_model(), on_delete=models.CASCADE)
     is_public = models.BooleanField(blank=False, null=False, default=False)
     shared_institutions = models.ManyToManyField(Institution, related_name='shared_differential_expression', blank=True)
diff --git a/src/differential_expression/service.py b/src/differential_expression/service.py
new file mode 100644
index 00000000..9dc391c9
--- /dev/null
+++ b/src/differential_expression/service.py
@@ -0,0 +1,290 @@
+from common.exceptions import EmptyDataset
+from differential_expression.models import DifferentialExpressionExperiment
+import pandas as pd
+import numpy as np
+import logging
+from common.typing import AbortEvent
+    
+import rpy2.robjects as robjects
+from rpy2.robjects.conversion import get_conversion, localconverter
+from rpy2.robjects.pandas2ri import converter
+from rpy2.robjects import pandas2ri
+from rpy2.robjects.packages import importr
+from itertools import combinations
+
+class DifferentialExpressionService:
+    def __init__(self, experiment: DifferentialExpressionExperiment, is_aborted: AbortEvent):
+        self.experiment = experiment
+        self.is_aborted = is_aborted
+
+    def perform_differential_expression(self) -> pd.DataFrame:
+        clinical_df, mrna_df = self._process_datasets()
+        
+        sample_column = 'SAMPLE_ID'
+        if sample_column in clinical_df.columns:
+            common_samples = sorted(set(mrna_df.columns) & set(clinical_df[sample_column]))
+            df_RNAseq_filtered = mrna_df[common_samples]
+            df_clinical_filtered = clinical_df[clinical_df[sample_column].isin(common_samples)]
+            df_clinical_filtered = df_clinical_filtered.set_index(sample_column).reindex(common_samples).reset_index()
+        else:
+            df_RNAseq_filtered = mrna_df
+            df_clinical_filtered = clinical_df
+            
+        try:
+            # Import R packages
+            limma = importr('limma')  # limma for differential expression
+            stats = importr('stats')  # stats for model matrix
+            base = importr('base')  # base R functions
+            
+            # 1. Validation: Ensure the clinical attribute has at least two categories
+            # This is necessary because differential expression requires at least two groups to compare.
+            unique_values = df_clinical_filtered[self.experiment.clinical_attribute].dropna().unique()
+            if len(unique_values) < 2:
+                raise ValueError(f"At least two categories are required in '{self.experiment.clinical_attribute}'.")
+            
+            # 2. Group vector creation
+            # Converts the clinical attribute to a categorical variable (factor in R).
+            # This tells the model to treat the values as groups, not as numeric values.
+            group_values = df_clinical_filtered[self.experiment.clinical_attribute].astype(str).values
+            group_levels = sorted(np.unique(group_values))  # Get all unique group names sorted
+            group_dict = {k: i for i, k in enumerate(group_levels)}  # Map group names to indices (not strictly needed)
+            group_factor = pd.Categorical(group_values, categories=group_levels)
+            
+            # 3. Conversion to R objects
+            # Converts the filtered log-expression data (Pandas DataFrame) to an R matrix.
+            with localconverter(get_conversion() + converter):
+                r_log_data = pandas2ri.py2rpy(df_RNAseq_filtered)
+            # Convert the group factor to an R factor vector
+            r_group = robjects.FactorVector(group_factor)
+            
+            # 4. Design matrix construction (no intercept)
+            # The design matrix encodes the group structure for the linear model.
+            # Using '~ 0 + group' means no intercept: each group gets its own column.
+            formula = robjects.Formula('~ 0 + group')
+            env = robjects.Environment()
+            env['group'] = r_group
+            r_design = stats.model_matrix(formula, env)
+            r_design.colnames = robjects.StrVector(group_levels)  # Set column names to group names
+            
+            # 5. Linear model fitting with limma
+            # Fit the linear model to estimate mean expression for each gene in each group.
+            fit = limma.lmFit(r_log_data, r_design)
+            
+            # 6. Create all possible pairwise contrasts (all-vs-all)
+            # For each pair of groups, create a contrast expression like 'groupB - groupA'.
+            pares = list(combinations(group_levels, 2))
+            contrastes = [f"{b} - {a}" for a, b in pares]
+            contrast_matrix = limma.makeContrasts(
+                contrasts=robjects.StrVector(contrastes),
+                levels=r_design
+            )
+            
+            # 7. Apply contrasts and empirical Bayes moderation
+            # Apply the contrasts to the fitted model, then use eBayes to stabilize variance estimates.
+            fit2 = limma.contrasts_fit(fit, contrast_matrix)
+            fit2 = limma.eBayes(fit2)
+            
+            # 8. Extract results for the first contrast
+            # Get the table of differential expression results for the first contrast (logFC, p-value, adjusted p-value, etc.).
+            results = limma.topTable(
+                fit2,
+                coef=1,  # First contrast
+                number=robjects.r('Inf'),  # All genes
+                adjust_method="BH"  # Benjamini-Hochberg adjustment
+            )
+            
+            # Convert the R data frame to a Pandas DataFrame for further analysis in Python.
+            results_df = pandas2ri.rpy2py(results)
+            return results_df
+        
+        except Exception as e:
+            logging.error(f"Error occurred during differential expression analysis: {e}")
+            raise
+
+    def _process_datasets(self):
+        """Process clinical and mRNA datasets for differential expression analysis."""
+        clinical_df = self.experiment.clinical_source.get_df()
+        mrna_df = self.experiment.mrna_source.get_df()
+
+        if clinical_df.empty or mrna_df.empty:
+            raise EmptyDataset("One or both datasets are empty.")
+
+        data_processing_service = DataProcessingService(
+            clinical_df=clinical_df,
+            mrna_df=mrna_df,
+            clinical_attribute=self.experiment.clinical_attribute,
+            threshold_percentile=self.experiment.threshold_percentile,
+            threshold=self.experiment.threshold
+        )
+
+        return data_processing_service.process_datasets()
+
+
+class DataProcessingService:
+    """
+    Service for processing clinical and RNA-Seq datasets.
+    """
+    
+    def __init__(self, 
+                 clinical_df: pd.DataFrame, 
+                 mrna_df: pd.DataFrame, 
+                 clinical_attribute: str, 
+                 threshold_percentile: float = 0.15,
+                 threshold : float = 1e-4):
+        
+        self.clinical_df = clinical_df
+        self.mrna_df = mrna_df
+        self.clinical_attribute = clinical_attribute
+        self.threshold_percentile = threshold_percentile
+        self.threshold = threshold
+
+    def validate_datasets(self):
+        """Validate the clinical and mRNA datasets.
+
+        Raises:
+            EmptyDataset: If either dataset is empty.
+        """
+        if self.clinical_df.empty:
+            raise EmptyDataset("Clinical dataset is empty.")
+        if self.mrna_df.empty:
+            raise EmptyDataset("mRNA dataset is empty.")
+
+    def _process_clinical_data(self) -> None:
+        """Process the clinical dataset.
+        This method filters the clinical dataset to keep only the relevant columns,
+        removes rows with NA values in the clinical attribute, and ensures that
+        the clinical attribute is in uppercase if it is of string type.
+        """
+        
+        ###### Procesar datos clínicos #####
+        # Reset index para convertir PATIENT_ID de índice a columna
+        clinical_df_reset = self.clinical_df.reset_index()
+        
+        # Create sample dataframe with SAMPLE_ID and PATIENT_ID
+        df_clinical_sample = clinical_df_reset[['SAMPLE_ID', 'PATIENT_ID']]
+        
+        # Create patient dataframe with PATIENT_ID and clinical attribute, removing NA values
+        df_clinical_patient = clinical_df_reset[['PATIENT_ID', self.clinical_attribute]].dropna(subset=[self.clinical_attribute])
+        
+        # Si la columna es de tipo texto, limpiar y convertir a mayúsculas
+        if df_clinical_patient[self.clinical_attribute].dtype == 'object':
+            # Eliminar espacios al inicio y al final, luego convertir a mayúsculas
+            df_clinical_patient[self.clinical_attribute] = df_clinical_patient[self.clinical_attribute].astype(
+                str).str.strip().str.upper()
+
+        # Eliminar filas duplicadas
+        df_clinical_patient = df_clinical_patient.drop_duplicates()
+        
+        ##### Procesar datos de muestra #####
+        # df_clinical_sample = self.clinical_df[['SAMPLE_ID', 'PATIENT_ID']]
+        
+        ##### Fusionar datos clínicos y de muestra #####
+        df_clinical = pd.merge(df_clinical_sample, df_clinical_patient, on='PATIENT_ID', how='inner')
+        df_clinical = df_clinical[['SAMPLE_ID', self.clinical_attribute]]
+
+        df_clinical = df_clinical.drop_duplicates()
+        
+        self.clinical_df = df_clinical
+        logging.info("Clinical data processed successfully.")
+
+
+    def _process_mrna_data(self) -> None:
+        """Process the mRNA dataset.
+        This method processes the mRNA dataset by renaming columns, removing duplicates,
+        filtering samples based on the clinical dataset, and cleaning up NA values.
+        """
+        
+        mrna_dataset = self.mrna_df.reset_index(names='Hugo_Symbol')
+        
+        # Eliminar duplicados manteniendo la primera ocurrencia
+        mrna_dataset = mrna_dataset.drop_duplicates(subset=['Hugo_Symbol'], keep='first')
+        
+        # Antes de la intersección, normalizar los SAMPLE_ID extrayendo solo la parte base
+        self.clinical_df['SAMPLE_ID'] = self.clinical_df['SAMPLE_ID'].str.rsplit('-', n=1).str[0]
+        
+        # Obtener valores de SAMPLE_ID del DataFrame de metadatos
+        valid_columns = list(set(mrna_dataset.columns) & set(self.clinical_df['SAMPLE_ID']))
+        
+        # Filtrar el dataset de RNA-Seq para mantener solo las columnas válidas
+        mrna_dataset = mrna_dataset[['Hugo_Symbol'] + valid_columns]
+        
+        # Eliminar filas con NA en los datos de expresión génica
+        # Eliminar filas donde Hugo_Symbol es NA
+        mrna_dataset = mrna_dataset.dropna(subset=['Hugo_Symbol'])
+
+        # Establecer Hugo_Symbol como índice y eliminar la columna
+        mrna_dataset = mrna_dataset.set_index('Hugo_Symbol')
+        
+        self.mrna_df = mrna_dataset
+        logging.info("mRNA data processed successfully.")
+
+    def _transform_to_log2(self) -> None:
+        """Transform mRNA data to log2 scale.
+        This method applies a log2 transformation to the mRNA dataset.
+        """
+        
+        if isinstance(self.mrna_df, pd.DataFrame):
+            has_negative = (self.mrna_df < 0).any().any()
+        else:
+            has_negative = np.any(self.mrna_df < 0)
+            
+        if has_negative:
+            logging.warning("Negative values found in mRNA dataset. Skipping log2 transformation.")
+        
+        # Apply log2 transformation
+        mrna_df_log2 = np.log2(self.mrna_df + 1)
+        
+        self.mrna_df = mrna_df_log2
+        logging.info("Log2 transformation applied to mRNA data.")
+        
+    def _filter_low_expression_genes(self) -> None:
+        """Filter out low-expression genes from the mRNA dataset.
+        This method removes genes whose maximum expression across samples is below
+        a specified percentile threshold.
+        """
+        
+        # Calculate the average expression for each gene (across all samples)
+        avg_expression = self.mrna_df.mean(axis=1)
+
+        # Calculate the threshold based on the percentile
+        threshold = np.percentile(avg_expression, self.threshold_percentile * 100)
+        
+        # Filter genes with average expression above or equal to the threshold
+        genes_to_keep = avg_expression >= threshold
+        self.mrna_df = self.mrna_df[genes_to_keep]
+        
+        self.mrna_df = self.mrna_df
+        logging.info(f"Filtered low-expression genes. Threshold: {threshold:.2f}")
+        
+    
+    def _filter_genes_by_variance(self) -> None:
+        """Filter genes based on variance.
+        This method removes genes whose variance across samples is below
+        a specified percentile threshold.
+        """
+        
+        # Calculate variance for each gene (row)
+        variances = self.mrna_df.var(axis=1)
+
+        # Filter out genes with variance below the threshold
+        genes_to_keep = variances > self.threshold
+        self.mrna_df = self.mrna_df[genes_to_keep]
+        logging.info(f"Filtered genes by variance. Threshold: {self.threshold:.2f}")
+        
+    
+    def process_datasets(self) -> tuple[pd.DataFrame, pd.DataFrame]:
+        """Process the clinical and mRNA datasets.
+        This method orchestrates the processing steps for both datasets.
+        
+        Returns:
+            Tuple containing the processed clinical and mRNA datasets.
+        """
+        
+        self.validate_datasets()
+        self._process_clinical_data()
+        self._process_mrna_data()
+        self._transform_to_log2()
+        self._filter_low_expression_genes()
+        self._filter_genes_by_variance()
+        
+        return self.clinical_df, self.mrna_df
\ No newline at end of file
diff --git a/src/differential_expression/tasks.py b/src/differential_expression/tasks.py
new file mode 100644
index 00000000..a5842d81
--- /dev/null
+++ b/src/differential_expression/tasks.py
@@ -0,0 +1,79 @@
+import logging
+import time
+from celery.contrib.abortable import AbortableTask
+from multiomics_intermediate.celery import app
+from django.conf import settings
+from api_service import models as api_models
+from time import sleep
+from differential_expression.models import DifferentialExpressionExperiment, DifferentialExpressionExperimentState
+from common.exceptions import EmptyDataset, ExperimentStopped
+from .service import DifferentialExpressionService
+
+@app.task(bind=True, base=AbortableTask, acks_late=True, reject_on_worker_lost=True,
+          soft_time_limit=settings.FS_SOFT_TIME_LIMIT)
+def eval_differential_expression_experiment(self, experiment_pk: int, ):
+    """Evaluate differential expression for a given experiment.
+
+    @param self: Self instance of the Celery task (available due to bind=True).
+    @param experiment_pk: Primary key of the experiment to evaluate.
+    """
+    # Check if the experiment exists
+    try:
+        experiment : DifferentialExpressionExperiment = DifferentialExpressionExperiment.objects.get(pk=experiment_pk)
+    except DifferentialExpressionExperiment.DoesNotExist:
+        logging.error(f'DifferentialExpressionExperiment {experiment_pk} does not exist')
+        return
+    
+    # Check if the experiment has reached the limit of attempts
+    if experiment.attempt >= 3:
+        logging.warning(f'DifferentialExpressionExperiment {experiment.pk} has reached attempts limit.')
+        experiment.state = DifferentialExpressionExperimentState.REACHED_ATTEMPTS_LIMIT
+        experiment.save(update_fields=['state'])
+        return
+    
+    # Increment the attempt and set the state of the experiment to IN_PROCESS
+    experiment.attempt += 1
+    experiment.state = DifferentialExpressionExperimentState.IN_PROCESS
+    experiment.save(update_fields=['attempt', 'state'])
+    
+    try:
+        logging.warning(f'Starting evaluation for DifferentialExpressionExperiment ID -> {experiment.pk}')
+
+        # Compute the differential expression experiment
+        start = time.time()
+
+        compute_differential_expression = DifferentialExpressionService(experiment, is_aborted=self.is_aborted)
+        compute_differential_expression.perform_differential_expression()
+
+        total_execution_time = time.time() - start
+        logging.info(f'DifferentialExpressionExperiment {experiment.pk} processed in {total_execution_time:.2f} seconds.')
+        
+        # If user cancel the experiment, discard changes
+        if self.is_aborted():
+            raise ExperimentStopped
+        
+        experiment.execution_time = total_execution_time
+        experiment.save(update_fields=['execution_time'])
+
+        experiment.state = DifferentialExpressionExperimentState.COMPLETED
+        experiment.save(update_fields=['state'])
+
+    except EmptyDataset:
+        logging.error(f'Empty dataset error for DifferentialExpressionExperiment {experiment.pk}')
+        experiment.state = DifferentialExpressionExperimentState.EMPTY_DATASET
+        experiment.save(update_fields=['state'])
+        return
+
+    except Exception as e:
+        logging.error(f'Error during evaluation of DifferentialExpressionExperiment {experiment.pk}: {e}')
+        experiment.state = DifferentialExpressionExperimentState.FINISHED_WITH_ERROR
+        experiment.save(update_fields=['state'])
+        raise e
+    finally:
+        # Ensure that the experiment is marked as finished
+        if self.is_aborted():
+            logging.info(f'Evaluation for DifferentialExpressionExperiment {experiment.pk} was aborted.')
+            experiment.state = DifferentialExpressionExperimentState.STOPPED
+            experiment.save(update_fields=['state'])
+        else:
+            logging.info(f'Evaluation for DifferentialExpressionExperiment {experiment.pk} completed successfully.')
\ No newline at end of file
diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index ba54be6c..7c36fc43 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -3,5 +3,6 @@
 
 urlpatterns = [
     path('', views.DifferentialExpressionList.as_view(), name='differential_expression_list'),
+    path('<int:pk>/', views.DifferentialExpressionDetail.as_view()),
     path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
 ]
\ No newline at end of file
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 498f680b..65c4bdaf 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -14,6 +14,36 @@
 from differential_expression.serializers import DifferentialExpressionExperimentSerializer
 from django_filters.rest_framework import DjangoFilterBackend
 from common.pagination import StandardResultsSetPagination
+from celery.contrib.abortable import AbortableAsyncResult
+from .tasks import eval_differential_expression_experiment
+
+
+class DifferentialExpressionDetail(generics.RetrieveAPIView):
+    """
+    Endpoint to retrieve a differential expression experiment.
+    """
+
+    def get_object(self) -> DifferentialExpressionExperiment:
+        """
+        Retrieve the differential expression experiment by its ID.
+        """
+        user = self.request.user
+        experiment_id = self.kwargs.get('pk')
+        experiment = get_object_or_404(DifferentialExpressionExperiment, pk=experiment_id)
+
+        # Check if the user has access to the experiment
+        if not (experiment.is_public or
+                experiment.user == user or
+                experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
+                experiment.shared_users.filter(id=user.id).exists()):
+            raise ValidationError('You do not have permission to access this experiment.')
+
+        print(experiment.clinical_source.get_attributes())
+
+        return experiment
+
+    serializer_class = DifferentialExpressionExperimentSerializer
+    permission_classes = [permissions.IsAuthenticated]
 
 class DifferentialExpressionList(generics.ListAPIView):
     """
@@ -26,7 +56,7 @@ def get_queryset(self):
         """
         user = self.request.user
         experiments = DifferentialExpressionExperiment.objects.filter(
-            # Q(is_public=True) |
+            Q(is_public=True) |
             Q(user=user) |
             Q(shared_institutions__institutionadministration__user=user) |
             Q(shared_users=user)
@@ -109,4 +139,17 @@ def post(self, request : Request):
                 user = request.user,
             )
 
+            # async_res: AbortableAsyncResult = eval_feature_selection_experiment.apply_async(
+            # (fs_experiment.pk, fit_fun_enum, fitness_function_parameters, algorithm_parameters,
+            #  cross_validation_parameters), queue='feature_selection')
+
+            # fs_experiment.task_id = async_res.task_id
+            # fs_experiment.save(update_fields=['task_id'])
+            
+            async_res : AbortableAsyncResult = eval_differential_expression_experiment.apply_async(
+                (experiment.pk,), queue='differential_expression')
+            
+            experiment.task_id = async_res.task_id
+            experiment.save(update_fields=['task_id'])
+
             return Response({'ok': True})
diff --git a/src/feature_selection/tasks.py b/src/feature_selection/tasks.py
index f2e8edd8..9da116da 100644
--- a/src/feature_selection/tasks.py
+++ b/src/feature_selection/tasks.py
@@ -62,7 +62,7 @@ def eval_feature_selection_experiment(self, experiment_pk: int, fit_fun_enum: Fi
         start = time.time()
         molecules_temp_file_path, clinical_temp_file_path, running_in_spark = prepare_and_compute_fs_experiment(
             experiment, fit_fun_enum, fitness_function_parameters, algorithm_parameters,
-            cross_validation_parameters, self.is_aborted
+            cross_validation_parameters, is_aborted=self.is_aborted
         )
         total_execution_time = time.time() - start
         logging.warning(f'FSExperiment {experiment.pk} total time -> {total_execution_time} seconds')

From a8f7240f3166792695464b7ac15806eb94dde82f Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Thu, 7 Aug 2025 23:36:29 -0300
Subject: [PATCH 04/47] Add JSON results storage for differential expression

Introduces a results_json JSONField to DifferentialExpressionExperiment for efficient storage of full differential expression results. Adds model methods for saving, retrieving, and filtering results, updates the serializer to expose results metadata, and modifies the service and task logic to save and handle results as JSON. Also updates .gitignore and improves mRNA data processing in the service.
---
 .gitignore                                    |  3 +-
 ...entialexpressionexperiment_results_json.py | 25 +++++++++
 src/differential_expression/models.py         | 54 +++++++++++++++++++
 src/differential_expression/serializers.py    | 33 +++++++++++-
 src/differential_expression/service.py        | 22 ++++----
 src/differential_expression/tasks.py          |  9 +++-
 6 files changed, 132 insertions(+), 14 deletions(-)
 create mode 100644 src/differential_expression/migrations/0004_differentialexpressionexperiment_results_json.py

diff --git a/.gitignore b/.gitignore
index 66e1db9b..251fde10 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,4 +12,5 @@ src/api_service/experiments/venv
 docker-compose.yml
 src/secretkey.txt
 docker-compose.mauri_dev.yml
-venv
\ No newline at end of file
+venv
+.DS_Store
\ No newline at end of file
diff --git a/src/differential_expression/migrations/0004_differentialexpressionexperiment_results_json.py b/src/differential_expression/migrations/0004_differentialexpressionexperiment_results_json.py
new file mode 100644
index 00000000..337e026b
--- /dev/null
+++ b/src/differential_expression/migrations/0004_differentialexpressionexperiment_results_json.py
@@ -0,0 +1,25 @@
+# Generated by Django 4.2.19 on 2025-08-08 02:26
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "differential_expression",
+            "0003_alter_differentialexpressionexperiment_state",
+        ),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="differentialexpressionexperiment",
+            name="results_json",
+            field=models.JSONField(
+                blank=True,
+                help_text="Complete differential expression results as JSON",
+                null=True,
+            ),
+        ),
+    ]
diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index e70e911e..0c3e84d0 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -75,4 +75,58 @@ def save(self, *args, **kwargs):
         #     raise ValueError(f"An experiment with the name '{self.name}' already exists.")
 
         super().save(*args, **kwargs)
+
+
+    # Results storage
+    # Store the complete differential expression results as JSON
+    # This is more efficient than individual records for large datasets
+    results_json = models.JSONField(blank=True, null=True, help_text='Complete differential expression results as JSON')
+    
+    def save_results(self, dataframe):
+        """
+        Save the differential expression DataFrame results as JSON.
+        
+        Args:
+            dataframe: pandas DataFrame with differential expression results
+        """
+        # Convert DataFrame to JSON format (records orientation)
+        self.results_json = dataframe.to_dict('records')
+        self.save(update_fields=['results_json'])
+    
+    def get_results_dataframe(self):
+        """
+        Retrieve results as a pandas DataFrame.
+        
+        Returns:
+            pandas.DataFrame: DataFrame with differential expression results
+        """
+        if not self.results_json:
+            return None
+            
+        import pandas as pd
+        return pd.DataFrame(self.results_json)
+    
+    def get_significant_genes(self, p_value_threshold=0.05, log_fc_threshold=1.0):
+        """
+        Get significantly differentially expressed genes.
+        
+        Args:
+            p_value_threshold: Maximum adjusted p-value (default 0.05)
+            log_fc_threshold: Minimum absolute log fold change (default 1.0)
+            
+        Returns:
+            list: List of gene records meeting the criteria
+        """
+        if not self.results_json:
+            return []
+            
+        significant_genes = []
+        for gene in self.results_json:
+            adj_p_val = gene.get('adj.P.Val', gene.get('adjusted_p_value', 1.0))
+            log_fc = abs(gene.get('logFC', gene.get('log_fold_change', 0.0)))
+            
+            if adj_p_val <= p_value_threshold and log_fc >= log_fc_threshold:
+                significant_genes.append(gene)
+                
+        return significant_genes
         
\ No newline at end of file
diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index 7ec6fb13..07bc989d 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -1,7 +1,7 @@
 from rest_framework import serializers
 
 from differential_expression.models import DifferentialExpressionExperiment
-from drf_writable_nested import WritableNestedModelSerializer
+from drf_writable_nested.serializers import WritableNestedModelSerializer
 
 
 class DifferentialExpressionExperimentSerializer(WritableNestedModelSerializer):
@@ -16,7 +16,36 @@ class DifferentialExpressionExperimentSerializer(WritableNestedModelSerializer):
     )
     clinical_source = serializers.CharField(max_length=255, required=False)
     mrna_source = serializers.CharField(max_length=255, required=False)
+    
+    # Results-related fields
+    results_json = serializers.JSONField(read_only=True)
+    has_results = serializers.SerializerMethodField()
+    results_count = serializers.SerializerMethodField()
+    significant_genes_count = serializers.SerializerMethodField()
 
     class Meta:
         model = DifferentialExpressionExperiment
-        fields = '__all__'
\ No newline at end of file
+        fields = '__all__'
+    
+    def get_has_results(self, obj):
+        """Check if the experiment has results."""
+        return obj.results_json is not None and len(obj.results_json) > 0
+    
+    def get_results_count(self, obj):
+        """Get the total number of genes in results."""
+        if obj.results_json:
+            return len(obj.results_json)
+        return 0
+    
+    def get_significant_genes_count(self, obj):
+        """Get the number of significant genes (adj.P.Val <= 0.05)."""
+        if not obj.results_json:
+            return 0
+        
+        significant_count = 0
+        for gene in obj.results_json:
+            adj_p_val = gene.get('adj.P.Val', gene.get('adjusted_p_value', 1.0))
+            if adj_p_val <= 0.05:
+                significant_count += 1
+        
+        return significant_count
\ No newline at end of file
diff --git a/src/differential_expression/service.py b/src/differential_expression/service.py
index 9dc391c9..9ec50aa4 100644
--- a/src/differential_expression/service.py
+++ b/src/differential_expression/service.py
@@ -95,7 +95,11 @@ def perform_differential_expression(self) -> pd.DataFrame:
             
             # Convert the R data frame to a Pandas DataFrame for further analysis in Python.
             results_df = pandas2ri.rpy2py(results)
-            return results_df
+            
+            top_genes = results_df.nsmallest(10, 'adj.P.Val')
+            top_genes_reset = top_genes.reset_index() 
+            
+            return top_genes_reset
         
         except Exception as e:
             logging.error(f"Error occurred during differential expression analysis: {e}")
@@ -194,10 +198,9 @@ def _process_mrna_data(self) -> None:
         filtering samples based on the clinical dataset, and cleaning up NA values.
         """
         
-        mrna_dataset = self.mrna_df.reset_index(names='Hugo_Symbol')
-        
+
         # Eliminar duplicados manteniendo la primera ocurrencia
-        mrna_dataset = mrna_dataset.drop_duplicates(subset=['Hugo_Symbol'], keep='first')
+        mrna_dataset = self.mrna_df.drop_duplicates(subset=['Standard_Symbol'], keep='first')
         
         # Antes de la intersección, normalizar los SAMPLE_ID extrayendo solo la parte base
         self.clinical_df['SAMPLE_ID'] = self.clinical_df['SAMPLE_ID'].str.rsplit('-', n=1).str[0]
@@ -206,14 +209,15 @@ def _process_mrna_data(self) -> None:
         valid_columns = list(set(mrna_dataset.columns) & set(self.clinical_df['SAMPLE_ID']))
         
         # Filtrar el dataset de RNA-Seq para mantener solo las columnas válidas
-        mrna_dataset = mrna_dataset[['Hugo_Symbol'] + valid_columns]
+        mrna_dataset = mrna_dataset[['Standard_Symbol'] + valid_columns]
         
         # Eliminar filas con NA en los datos de expresión génica
-        # Eliminar filas donde Hugo_Symbol es NA
-        mrna_dataset = mrna_dataset.dropna(subset=['Hugo_Symbol'])
+        # Eliminar filas donde Standard_Symbol es NA
+        mrna_dataset = mrna_dataset.dropna(subset=['Standard_Symbol'])
 
-        # Establecer Hugo_Symbol como índice y eliminar la columna
-        mrna_dataset = mrna_dataset.set_index('Hugo_Symbol')
+        # Establecer Standard_Symbol como índice con el nombre Hugo_Symbol y eliminar la columna
+        mrna_dataset = mrna_dataset.set_index('Standard_Symbol')
+        mrna_dataset.index.name = 'Hugo_Symbol'
         
         self.mrna_df = mrna_dataset
         logging.info("mRNA data processed successfully.")
diff --git a/src/differential_expression/tasks.py b/src/differential_expression/tasks.py
index a5842d81..d99d2bd3 100644
--- a/src/differential_expression/tasks.py
+++ b/src/differential_expression/tasks.py
@@ -43,8 +43,8 @@ def eval_differential_expression_experiment(self, experiment_pk: int, ):
         start = time.time()
 
         compute_differential_expression = DifferentialExpressionService(experiment, is_aborted=self.is_aborted)
-        compute_differential_expression.perform_differential_expression()
-
+        result = compute_differential_expression.perform_differential_expression()
+        print(f'Result of differential expression computation: {result}')
         total_execution_time = time.time() - start
         logging.info(f'DifferentialExpressionExperiment {experiment.pk} processed in {total_execution_time:.2f} seconds.')
         
@@ -52,6 +52,11 @@ def eval_differential_expression_experiment(self, experiment_pk: int, ):
         if self.is_aborted():
             raise ExperimentStopped
         
+        # Save the results to the database if we got results
+        if result is not None:
+            experiment.save_results(result)
+            logging.info(f'Results saved for DifferentialExpressionExperiment {experiment.pk}')
+        
         experiment.execution_time = total_execution_time
         experiment.save(update_fields=['execution_time'])
 

From 73e31516fa05e43fd895269c72025a0ec83a1317 Mon Sep 17 00:00:00 2001
From: Juan <juannicolash01@gmail.com>
Date: Fri, 8 Aug 2025 16:25:31 -0300
Subject: [PATCH 05/47] save 8-8

---
 .../DifferentialExpressionForm.tsx            | 249 ++++++++++++++++--
 .../DifferentialExpressionPanel.tsx           |  12 +-
 .../src/css/differential-expression.css       |  10 +
 3 files changed, 243 insertions(+), 28 deletions(-)

diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
index b50f5638..7288c424 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
@@ -1,56 +1,251 @@
-import React from 'react'
-import { Input, TextArea } from 'semantic-ui-react'
+import React, { useState } from 'react'
+import { Form, Header, Icon, Input, Label, Segment, TextArea } from 'semantic-ui-react'
 import { SourceForm } from '../pipeline/SourceForm'
+import { SingleRangeSlider } from 'neo-react-semantic-ui-range'
+import { FileType, Source, SourceType } from '../../utils/interfaces'
+import { cleanRef, getDefaultSource, getFilenameFromSource } from '../../utils/util_functions'
+import { DjangoCGDSStudy, DjangoUserFile } from '../../utils/django_interfaces'
+
+interface IDifferentialExpressionForm extends IDifferentialExpressionFormData {
+    isEditing: boolean
+}
+
+/** Available types of Sources for a DifferentialExpressionForm. */
+type SourceStateDifferentialExpression = 'clinicalSource' | 'mRNASource'
+
+/** Structure for the Feature Selection panel. */
+interface IDifferentialExpressionFormData {
+    /** mRNA source. */
+    mRNASource: Source,
+    /** clinical source. */
+    clinicalSource: Source,
+    /** Differential Expression name. */
+    differentialExpressionDescription: string,
+    /** Differential Expression description. */
+    differentialExpressionName: string,
+    /** Percentile threshold. */
+    percentileThreshold: number,
+
+}
+const cleanForm: IDifferentialExpressionForm = {
+    mRNASource: getDefaultSource(),
+    clinicalSource: getDefaultSource(),
+    isEditing: false,
+    differentialExpressionDescription: '',
+    differentialExpressionName: '',
+    percentileThreshold: 0.15,
+}
 
 export const DifferentialExpressionForm = () => {
+    const [form, setForm] = useState<IDifferentialExpressionForm>(cleanForm);
+
+    /**
+     * Change the source state to submit a pipeline
+     * @param sourceType New selected Source
+     * @param sourceStateName Source's name in state object to update
+     */
+    const handleChangeSourceType = (sourceType: SourceType, sourceStateName: SourceStateDifferentialExpression) => {
+        // Selects source to update
+        const source = form[sourceStateName]
+        // Change source type
+        source.type = sourceType
+
+        // Resets all source values
+        source.selectedExistingFile = null
+        source.CGDSStudy = null
+        cleanRef(source.newUploadedFileRef)
+        console.log(source)
+        console.log('---')
+        // After update state
+        setForm(prevState => ({
+            ...prevState,
+            [sourceStateName]: source,
+        }))
+        console.log(form)
+        console.log('---')
+
+        updateSourceFilenamesAndCommonSamples()
+    }
+
+    /**
+     * Selects a User's file as a source
+     * @param selectedFile Selected file as Source
+     * @param sourceStateName Source's name in state object to update
+     */
+    const selectUploadedFile = (selectedFile: DjangoUserFile, sourceStateName: SourceStateDifferentialExpression) => {
+        // Selects source to update
+        const source = form[sourceStateName]
+
+        source.type = SourceType.UPLOADED_DATASETS
+        source.selectedExistingFile = selectedFile
+        setForm(prevState => ({
+            ...prevState,
+            [sourceStateName]: source,
+        }))
+        updateSourceFilenamesAndCommonSamples()
+    }
+
+    /**
+     * Selects a CGDS Study as a source
+     * @param selectedStudy Selected Study as Source
+     * @param sourceStateName Source's name in state object to update
+     */
+    const selectStudy = (selectedStudy: DjangoCGDSStudy, sourceStateName: SourceStateDifferentialExpression) => {
+        // Selects source to update
+        const source = form[sourceStateName]
+
+        source.type = SourceType.CGDS
+        source.CGDSStudy = selectedStudy
+        setForm(prevState => ({
+            ...prevState,
+            [sourceStateName]: source,
+        }))
+        updateSourceFilenamesAndCommonSamples()
+    }
+
+
+    /**
+     * Handles file input changes to set data to show in form
+     * IMPORTANT: this is necessary because the file inputs are uncontrolled components
+     * and doesn't trigger an update of the state fields
+     */
+    const updateSourceFilenames = () => {
+        setForm(prevState => ({
+            ...prevState,
+            clinicalSource: {
+                ...prevState.clinicalSource,
+                filename: getFilenameFromSource(prevState.clinicalSource)
+            },
+            mRNASource: {
+                ...prevState.mRNASource,
+                filename: getFilenameFromSource(prevState.mRNASource)
+            },
+
+        }))
+    }
+
+    /**
+     * Callback when a new file is selected in the uncontrolled component
+     * (input type=file)
+     */
+    const updateSourceFilenamesAndCommonSamples = () => {
+        updateSourceFilenames()
+    }
+
+
+    /**
+ * Callback when a new file is selected in the uncontrolled component
+ * (input type=file)
+ */
+    const selectNewFile = () => { updateSourceFilenamesAndCommonSamples() }
+
+    /**
+     * change name or description of manual form
+     * @param value new value for input form
+     * @param name type of input to change
+     */
+    const handleChangeForm = (value: string | number, name: 'differentialExpressionName' | 'differentialExpressionDescription' | 'coefficientThreshold') => {
+        setForm(prevState => ({
+            ...prevState,
+            [name]: value,
+        }))
+    }
+
     return (
-        <div>
-            <Input placeholder='Search...' />
-            <TextArea placeholder='Tell us more' />
+        <Segment className='diff--side--bar--container table-bordered'>
+            <Header textAlign='center' className='margin-top-0'>
+                <Icon name='th' />
+                <Header.Content>New Differential Expression</Header.Content>
+            </Header>
+            <Input
+                onChange={(e) => handleChangeForm(e.target.value, 'differentialExpressionName')}
+                type='text'
+                placeholder='Name'
+                className='diff--side--bar--container--item--margin'
+                value={form.differentialExpressionName}
+                icon='asterisk'
+            />
+
+            <TextArea
+                style={{ maxWidth: '100%', minWidth: '100%' }}
+                rows={3}
+                onChange={(_, e) => handleChangeForm(e.value ? e.value.toString() : '', 'differentialExpressionDescription')}
+                placeholder='Description'
+                className='diff--side--bar--container--item--margin'
+                value={form.differentialExpressionDescription}
+            />
             {/* mRNA SourceForm */}
-           {/*  <SourceForm
-                source={newExperiment.mRNASource}
+            <SourceForm
+                source={form.mRNASource}
                 headerTitle='mRNA profile'
                 headerIcon={{
                     type: 'img',
                     src: 'static/frontend/img/profiles/mRNA.svg'
                 }}
                 fileType={FileType.MRNA}
-                disabled={isEditing}
-                tagOptions={this.props.tagOptions}
+                disabled={form.isEditing}
+                tagOptions={[]}
                 handleChangeSourceType={(selectedSourceType) => {
-                    this.props.handleChangeSourceType(selectedSourceType, 'mRNASource')
+                    handleChangeSourceType(selectedSourceType, 'mRNASource')
                 }}
-                selectNewFile={this.props.selectNewFile}
+                selectNewFile={selectNewFile}
                 selectUploadedFile={(selectedFile) => {
-                    this.props.selectUploadedFile(selectedFile, 'mRNASource')
+                    selectUploadedFile(selectedFile, 'mRNASource')
                 }}
                 selectStudy={(selectedStudy) => {
-                    this.props.selectStudy(selectedStudy, 'mRNASource')
+                    selectStudy(selectedStudy, 'mRNASource')
                 }}
-            /> */}
+            />
             {/* Clinical SourceForm */}
-           {/*  <SourceForm
-                source={newExperiment.mRNASource}
-                headerTitle='mRNA profile'
+            <SourceForm
+                source={form.clinicalSource}
+                headerTitle='Clinical profile'
                 headerIcon={{
                     type: 'img',
-                    src: 'static/frontend/img/profiles/mRNA.svg'
+                    src: '/static/frontend/img/profiles/mRNA.svg'
                 }}
-                fileType={FileType.MRNA}
-                disabled={isEditing}
-                tagOptions={this.props.tagOptions}
+                fileType={FileType.CLINICAL}
+                disabled={form.isEditing}
+                tagOptions={[]}
                 handleChangeSourceType={(selectedSourceType) => {
-                    this.props.handleChangeSourceType(selectedSourceType, 'mRNASource')
+                    handleChangeSourceType(selectedSourceType, 'clinicalSource')
                 }}
-                selectNewFile={this.props.selectNewFile}
+                selectNewFile={selectNewFile}
                 selectUploadedFile={(selectedFile) => {
-                    this.props.selectUploadedFile(selectedFile, 'mRNASource')
+                    selectUploadedFile(selectedFile, 'clinicalSource')
                 }}
                 selectStudy={(selectedStudy) => {
-                    this.props.selectStudy(selectedStudy, 'mRNASource')
+                    selectStudy(selectedStudy, 'clinicalSource')
                 }}
-            /> */}
-        </div>
+            />
+
+            <Form.Field width={6}>
+                <Label
+                    id='slider-cor-filter-label'
+                    className='align-center bolder'
+                >
+                    Percentile threshold {form.percentileThreshold.toFixed(2)}
+                </Label>
+
+                <SingleRangeSlider
+                    value={form.percentileThreshold}
+                    color='green'
+                    defaultMinValue={0}
+                    className='margin-bottom-5'
+                    defaultMaxValue={1}
+                    step={0.05}
+                    onChange={(value: number) => handleChangeForm(value, 'coefficientThreshold')}
+                />
+
+                <Label
+                    id='label-minimum-threshold'
+                    color='green'
+                    className='pull-left'
+                >
+                    {form.percentileThreshold.toFixed(2)}
+                </Label>
+                <Label color='green' className='pull-right'>1</Label>
+            </Form.Field>
+        </Segment>
     )
 }
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index 33611d89..85792b56 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -1,11 +1,21 @@
 import React from 'react'
 import { Base } from '../Base'
 import { DifferentialExpressionForm } from './DifferentialExpressionForm'
+import { Grid } from 'semantic-ui-react'
 
 export const DiferentialExpressionPanel = () => {
     return (
         <Base activeItem='differential-expression' wrapperClass='wrapper'>
-            <DifferentialExpressionForm />
+            <Grid columns={2} padded stackable divided className='biomarkers--modal--container'>
+                <Grid.Column width={4} textAlign='center'>
+
+                    <DifferentialExpressionForm />
+
+                </Grid.Column>
+                <Grid.Column width={12}>
+
+                </Grid.Column>
+            </Grid>
         </Base>
     )
 }
diff --git a/src/frontend/static/frontend/src/css/differential-expression.css b/src/frontend/static/frontend/src/css/differential-expression.css
index e69de29b..3314f289 100644
--- a/src/frontend/static/frontend/src/css/differential-expression.css
+++ b/src/frontend/static/frontend/src/css/differential-expression.css
@@ -0,0 +1,10 @@
+.diff--side--bar--container {
+    display: flex;
+    flex-direction: column;
+    width: 100%;
+    height: 100%;
+}
+
+.diff--side--bar--container--item--margin {
+    margin: 0.5rem 0;
+}
\ No newline at end of file

From b68181d33a65191218711d671c78e2ea263b982c Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Wed, 13 Aug 2025 22:24:24 -0300
Subject: [PATCH 06/47] Refactor differential expression models and API

Major refactor of differential expression models to use dedicated Source and ClinicalSource models, and store experiment results in a normalized table instead of JSON. Updated admin, serializers, views, and service logic to support new data model and endpoints for results and significant genes. Removed obsolete migrations and added new migration for timestamp fields. Improved mRNA/clinical data processing and result handling.
---
 src/differential_expression/admin.py          | 195 +++++++++++
 .../migrations/0001_initial.py                | 239 ++++++++++++-
 ...alexpressionexperiment_attempt_and_more.py |  59 ----
 ...xpressionexperiment_created_at_and_more.py |  31 ++
 ..._differentialexpressionexperiment_state.py |  37 --
 ...entialexpressionexperiment_results_json.py |  25 --
 src/differential_expression/models.py         | 330 ++++++++++++++++--
 src/differential_expression/serializers.py    | 197 +++++++++--
 src/differential_expression/service.py        |  41 ++-
 src/differential_expression/urls.py           |   2 +
 src/differential_expression/utils.py          |   0
 src/differential_expression/views.py          | 225 +++++++++---
 .../frontend/differential-expression.html     |  22 +-
 src/frontend/views.py                         |   9 +-
 14 files changed, 1165 insertions(+), 247 deletions(-)
 delete mode 100644 src/differential_expression/migrations/0002_differentialexpressionexperiment_attempt_and_more.py
 create mode 100644 src/differential_expression/migrations/0002_differentialexpressionexperiment_created_at_and_more.py
 delete mode 100644 src/differential_expression/migrations/0003_alter_differentialexpressionexperiment_state.py
 delete mode 100644 src/differential_expression/migrations/0004_differentialexpressionexperiment_results_json.py
 create mode 100644 src/differential_expression/utils.py

diff --git a/src/differential_expression/admin.py b/src/differential_expression/admin.py
index f1244222..4a6ec737 100644
--- a/src/differential_expression/admin.py
+++ b/src/differential_expression/admin.py
@@ -1 +1,196 @@
 from django.contrib import admin
+from .models import (
+    DifferentialExpressionSource,
+    DifferentialExpressionClinicalSource,
+    DifferentialExpressionExperiment,
+    DifferentialExpressionExperimentResult
+)
+
+
+@admin.register(DifferentialExpressionSource)
+class DifferentialExpressionSourceAdmin(admin.ModelAdmin):
+    """Admin configuration for DifferentialExpressionSource model."""
+    
+    list_display = ('id', 'get_source_type', 'get_source_name', 'number_of_samples', 'number_of_rows')
+    list_filter = ('user_file__file_type',)  # Removed cgds_dataset__file_type as it might not exist
+    search_fields = ('user_file__name', 'cgds_dataset__name', 'user_file__user__username')
+    readonly_fields = ('id', 'number_of_samples', 'number_of_rows')
+    
+    fieldsets = (
+        ('Source Information', {
+            'fields': ('id', 'user_file', 'cgds_dataset')
+        }),
+        ('Statistics', {
+            'fields': ('number_of_samples', 'number_of_rows'),
+            'classes': ('collapse',)
+        }),
+    )
+    
+    def get_source_type(self, obj):
+        """Returns the type of source (UserFile or CGDS)."""
+        if obj.user_file:
+            return f"User File ({obj.user_file.file_type})"
+        elif obj.cgds_dataset:
+            return f"CGDS Dataset ({obj.cgds_dataset.file_type})"
+        return "No source"
+    get_source_type.short_description = 'Source Type'
+    
+    def get_source_name(self, obj):
+        """Returns the name of the source."""
+        try:
+            valid_source = obj.get_valid_source()
+            return valid_source.name if hasattr(valid_source, 'name') else str(valid_source)
+        except:
+            return "No source"
+    get_source_name.short_description = 'Source Name'
+
+
+@admin.register(DifferentialExpressionClinicalSource)
+class DifferentialExpressionClinicalSourceAdmin(admin.ModelAdmin):
+    """Admin configuration for DifferentialExpressionClinicalSource model."""
+    
+    list_display = ('id', 'get_source_type', 'get_source_name', 'get_attributes_count', 'number_of_samples')
+    list_filter = ('user_file__file_type',)  # Removed cgds_dataset__file_type as it might not exist
+    search_fields = ('user_file__name', 'cgds_dataset__name', 'user_file__user__username')
+    readonly_fields = ('id', 'number_of_samples', 'number_of_rows', 'get_attributes_count')
+    
+    fieldsets = (
+        ('Source Information', {
+            'fields': ('id', 'user_file', 'cgds_dataset', 'extra_cgds_dataset')
+        }),
+        ('Statistics', {
+            'fields': ('number_of_samples', 'number_of_rows', 'get_attributes_count'),
+            'classes': ('collapse',)
+        }),
+    )
+    
+    def get_source_type(self, obj):
+        """Returns the type of clinical source."""
+        if obj.user_file:
+            return f"User File ({obj.user_file.file_type})"
+        elif obj.cgds_dataset and obj.extra_cgds_dataset:
+            return "CGDS Clinical (Patient + Sample)"
+        elif obj.cgds_dataset:
+            return "CGDS Clinical (Patient only)"
+        return "No source"
+    get_source_type.short_description = 'Clinical Source Type'
+    
+    def get_source_name(self, obj):
+        """Returns the name of the clinical source."""
+        try:
+            if obj.user_file:
+                return obj.user_file.name
+            elif obj.cgds_dataset:
+                return obj.cgds_dataset.name
+            return "No source"
+        except:
+            return "No source"
+    get_source_name.short_description = 'Source Name'
+    
+    def get_attributes_count(self, obj):
+        """Returns the number of clinical attributes."""
+        try:
+            return len(obj.get_attributes())
+        except:
+            return 0
+    get_attributes_count.short_description = 'Clinical Attributes Count'
+
+
+@admin.register(DifferentialExpressionExperiment)
+class DifferentialExpressionExperimentAdmin(admin.ModelAdmin):
+    """Admin configuration for DifferentialExpressionExperiment model."""
+    
+    list_display = (
+        'id', 'name', 'user', 'state', 'clinical_attribute', 
+        'threshold_percentile', 'threshold', 'execution_time', 'created_at'
+    )
+    list_filter = (
+        'state', 'is_public', 'clinical_attribute', 'created_at'
+    )
+    search_fields = ('name', 'description', 'user__username', 'clinical_attribute')
+    readonly_fields = (
+        'id', 'task_id', 'execution_time', 'attempt', 'created_at', 'updated_at',
+        'get_results_count', 'get_significant_genes_count'
+    )
+    filter_horizontal = ('shared_institutions', 'shared_users')
+    
+    fieldsets = (
+        ('Basic Information', {
+            'fields': ('id', 'name', 'description', 'user')
+        }),
+        ('Data Sources', {
+            'fields': ('clinical_source', 'mrna_source')
+        }),
+        ('Analysis Parameters', {
+            'fields': ('clinical_attribute', 'threshold_percentile', 'threshold')
+        }),
+        ('Execution Information', {
+            'fields': ('state', 'task_id', 'execution_time', 'attempt', 'created_at', 'updated_at'),
+            'classes': ('collapse',)
+        }),
+        ('Results Statistics', {
+            'fields': ('get_results_count', 'get_significant_genes_count'),
+            'classes': ('collapse',)
+        }),
+        ('Sharing', {
+            'fields': ('is_public', 'shared_institutions', 'shared_users'),
+            'classes': ('collapse',)
+        }),
+    )
+    
+    def get_results_count(self, obj):
+        """Returns the total number of results."""
+        try:
+            return obj.results.count()
+        except:
+            return 0
+    get_results_count.short_description = 'Total Results'
+    
+    def get_significant_genes_count(self, obj):
+        """Returns the number of significant genes with default thresholds."""
+        try:
+            return obj.get_significant_genes().count()
+        except:
+            return 0
+    get_significant_genes_count.short_description = 'Significant Genes (p<0.05, |logFC|>1)'
+
+
+@admin.register(DifferentialExpressionExperimentResult)
+class DifferentialExpressionExperimentResultAdmin(admin.ModelAdmin):
+    """Admin configuration for DifferentialExpressionExperimentResult model."""
+    
+    list_display = (
+        'id', 'experiment', 'gene', 'adj_p_val', 'log_fc', 
+        'p_value', 'ave_expr', 'is_significant_display'
+    )
+    list_filter = ('experiment__state', 'experiment__user')
+    search_fields = ('gene', 'experiment__name', 'experiment__user__username')
+    readonly_fields = ('id', 'is_significant_display')
+    
+    fieldsets = (
+        ('Basic Information', {
+            'fields': ('id', 'experiment', 'gene')
+        }),
+        ('Statistical Results', {
+            'fields': ('p_value', 'adj_p_val', 'log_fc', 'ave_expr', 't_statistic', 'b_statistic')
+        }),
+        ('Significance', {
+            'fields': ('is_significant_display',),
+            'classes': ('collapse',)
+        }),
+    )
+    
+    def is_significant_display(self, obj):
+        """Display if the gene is significant with default thresholds."""
+        try:
+            return obj.is_significant()
+        except:
+            return False
+    is_significant_display.short_description = 'Is Significant (p<0.05, |logFC|>1)'
+    is_significant_display.boolean = True
+
+
+# Custom admin site configuration
+admin.site.site_header = "Multiomix Administration"
+admin.site.site_title = "Multiomix Admin"
+admin.site.index_title = "Welcome to Multiomix Administration"
diff --git a/src/differential_expression/migrations/0001_initial.py b/src/differential_expression/migrations/0001_initial.py
index 6910afbc..7aacd5d0 100644
--- a/src/differential_expression/migrations/0001_initial.py
+++ b/src/differential_expression/migrations/0001_initial.py
@@ -1,4 +1,4 @@
-# Generated by Django 4.2.19 on 2025-08-03 19:37
+# Generated by Django 4.2.19 on 2025-08-09 18:54
 
 from django.conf import settings
 from django.db import migrations, models
@@ -10,28 +10,233 @@ class Migration(migrations.Migration):
     initial = True
 
     dependencies = [
-        ('institutions', '0005_alter_institution_options_and_more'),
         migrations.swappable_dependency(settings.AUTH_USER_MODEL),
-        ('api_service', '0061_alter_experiment_shared_users'),
+        ("institutions", "0005_alter_institution_options_and_more"),
+        ("user_files", "0015_alter_userfile_options"),
+        ("datasets_synchronization", "0035_auto_20230922_2356"),
     ]
 
     operations = [
         migrations.CreateModel(
-            name='DifferentialExpressionExperiment',
+            name="DifferentialExpressionSource",
             fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('name', models.CharField(max_length=300)),
-                ('description', models.TextField(blank=True, null=True)),
-                ('clinical_attribute', models.CharField(max_length=100)),
-                ('threshold_percentile', models.FloatField(default=0.15)),
-                ('threshold', models.FloatField(default=0.0001)),
-                ('task_id', models.CharField(blank=True, max_length=100, null=True)),
-                ('is_public', models.BooleanField(default=False)),
-                ('clinical_source', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='differential_expression_as_clinical', to='api_service.experimentclinicalsource')),
-                ('mrna_source', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='differential_expression_as_mrna', to='api_service.experimentsource')),
-                ('shared_institutions', models.ManyToManyField(blank=True, related_name='shared_differential_expression', to='institutions.institution')),
-                ('shared_users', models.ManyToManyField(blank=True, related_name='shared_users_differential_expression', to=settings.AUTH_USER_MODEL)),
-                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                (
+                    "cgds_dataset",
+                    models.ForeignKey(
+                        blank=True,
+                        null=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="differential_expression_sources",
+                        to="datasets_synchronization.cgdsdataset",
+                    ),
+                ),
+                (
+                    "user_file",
+                    models.ForeignKey(
+                        blank=True,
+                        null=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="differential_expression_sources",
+                        to="user_files.userfile",
+                    ),
+                ),
             ],
         ),
+        migrations.CreateModel(
+            name="DifferentialExpressionClinicalSource",
+            fields=[
+                (
+                    "differentialexpressionsource_ptr",
+                    models.OneToOneField(
+                        auto_created=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        parent_link=True,
+                        primary_key=True,
+                        serialize=False,
+                        to="differential_expression.differentialexpressionsource",
+                    ),
+                ),
+                (
+                    "extra_cgds_dataset",
+                    models.ForeignKey(
+                        blank=True,
+                        null=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="differential_expression_clinical_sources_extra",
+                        to="datasets_synchronization.cgdsdataset",
+                    ),
+                ),
+            ],
+            bases=("differential_expression.differentialexpressionsource",),
+        ),
+        migrations.CreateModel(
+            name="DifferentialExpressionExperiment",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("name", models.CharField(max_length=300)),
+                ("description", models.TextField(blank=True, null=True)),
+                ("clinical_attribute", models.CharField(max_length=100)),
+                ("threshold_percentile", models.FloatField(default=0.15)),
+                ("threshold", models.FloatField(default=0.0001)),
+                (
+                    "execution_time",
+                    models.FloatField(
+                        blank=True,
+                        default=0.0,
+                        help_text="Execution time in seconds",
+                        null=True,
+                    ),
+                ),
+                (
+                    "task_id",
+                    models.CharField(
+                        blank=True,
+                        help_text="Celery Task ID",
+                        max_length=100,
+                        null=True,
+                    ),
+                ),
+                (
+                    "attempt",
+                    models.PositiveSmallIntegerField(
+                        default=0,
+                        help_text="Number of attempts to prevent a buggy experiment running forever",
+                    ),
+                ),
+                (
+                    "state",
+                    models.IntegerField(
+                        choices=[
+                            (1, "Completed"),
+                            (2, "Finished With Error"),
+                            (3, "In Process"),
+                            (4, "Waiting For Queue"),
+                            (5, "No Samples In Common"),
+                            (6, "Stopping"),
+                            (7, "Stopped"),
+                            (8, "Reached Attempts Limit"),
+                            (9, "No Features Found"),
+                            (10, "Empty Dataset"),
+                            (11, "Timeout Exceeded"),
+                        ],
+                        default=4,
+                        help_text="Current state of the differential expression experiment",
+                    ),
+                ),
+                ("is_public", models.BooleanField(default=False)),
+                (
+                    "mrna_source",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="differential_expression_experiments_as_mrna",
+                        to="differential_expression.differentialexpressionsource",
+                    ),
+                ),
+                (
+                    "shared_institutions",
+                    models.ManyToManyField(
+                        blank=True,
+                        related_name="shared_differential_expression",
+                        to="institutions.institution",
+                    ),
+                ),
+                (
+                    "shared_users",
+                    models.ManyToManyField(
+                        blank=True,
+                        related_name="shared_users_differential_expression",
+                        to=settings.AUTH_USER_MODEL,
+                    ),
+                ),
+                (
+                    "user",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        to=settings.AUTH_USER_MODEL,
+                    ),
+                ),
+                (
+                    "clinical_source",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="differential_expression_experiments_as_clinical",
+                        to="differential_expression.differentialexpressionclinicalsource",
+                    ),
+                ),
+            ],
+        ),
+        migrations.CreateModel(
+            name="DifferentialExpressionExperimentResult",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("gene", models.CharField(help_text="Gene identifier", max_length=100)),
+                ("ave_expr", models.FloatField(help_text="Average expression level")),
+                (
+                    "p_value",
+                    models.FloatField(help_text="P-value from statistical test"),
+                ),
+                (
+                    "adj_p_val",
+                    models.FloatField(help_text="Adjusted P-value (FDR corrected)"),
+                ),
+                ("log_fc", models.FloatField(help_text="Log fold change")),
+                (
+                    "t_statistic",
+                    models.FloatField(help_text="t-statistic from the test"),
+                ),
+                (
+                    "b_statistic",
+                    models.FloatField(
+                        help_text="B-statistic (log-odds of differential expression)"
+                    ),
+                ),
+                (
+                    "experiment",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="results",
+                        to="differential_expression.differentialexpressionexperiment",
+                    ),
+                ),
+            ],
+            options={
+                "indexes": [
+                    models.Index(
+                        fields=["experiment", "adj_p_val"],
+                        name="differentia_experim_c0aff3_idx",
+                    ),
+                    models.Index(
+                        fields=["experiment", "log_fc"],
+                        name="differentia_experim_084601_idx",
+                    ),
+                    models.Index(fields=["gene"], name="differentia_gene_7c8c66_idx"),
+                ],
+                "unique_together": {("experiment", "gene")},
+            },
+        ),
     ]
diff --git a/src/differential_expression/migrations/0002_differentialexpressionexperiment_attempt_and_more.py b/src/differential_expression/migrations/0002_differentialexpressionexperiment_attempt_and_more.py
deleted file mode 100644
index f7429abb..00000000
--- a/src/differential_expression/migrations/0002_differentialexpressionexperiment_attempt_and_more.py
+++ /dev/null
@@ -1,59 +0,0 @@
-# Generated by Django 4.2.19 on 2025-08-05 01:30
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ("differential_expression", "0001_initial"),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="differentialexpressionexperiment",
-            name="attempt",
-            field=models.PositiveSmallIntegerField(
-                default=0,
-                help_text="Number of attempts to prevent a buggy experiment running forever",
-            ),
-        ),
-        migrations.AddField(
-            model_name="differentialexpressionexperiment",
-            name="execution_time",
-            field=models.FloatField(
-                blank=True,
-                default=0.0,
-                help_text="Execution time in seconds",
-                null=True,
-            ),
-        ),
-        migrations.AddField(
-            model_name="differentialexpressionexperiment",
-            name="state",
-            field=models.IntegerField(
-                choices=[
-                    (1, "Completed"),
-                    (2, "Finished With Error"),
-                    (3, "In Process"),
-                    (4, "Waiting For Queue"),
-                    (5, "No Samples In Common"),
-                    (6, "Stopping"),
-                    (7, "Stopped"),
-                    (8, "Reached Attempts Limit"),
-                    (9, "No Features Found"),
-                    (10, "Empty Dataset"),
-                    (11, "Timeout Exceeded"),
-                ],
-                default=4,
-                help_text="State of the differential expression experiment",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="differentialexpressionexperiment",
-            name="task_id",
-            field=models.CharField(
-                blank=True, help_text="Celery Task ID", max_length=100, null=True
-            ),
-        ),
-    ]
diff --git a/src/differential_expression/migrations/0002_differentialexpressionexperiment_created_at_and_more.py b/src/differential_expression/migrations/0002_differentialexpressionexperiment_created_at_and_more.py
new file mode 100644
index 00000000..ca3040ca
--- /dev/null
+++ b/src/differential_expression/migrations/0002_differentialexpressionexperiment_created_at_and_more.py
@@ -0,0 +1,31 @@
+# Generated by Django 4.2.19 on 2025-08-09 19:01
+
+from django.db import migrations, models
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("differential_expression", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="differentialexpressionexperiment",
+            name="created_at",
+            field=models.DateTimeField(
+                auto_now_add=True,
+                default=django.utils.timezone.now,
+                help_text="When the experiment was created",
+            ),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name="differentialexpressionexperiment",
+            name="updated_at",
+            field=models.DateTimeField(
+                auto_now=True, help_text="When the experiment was last updated"
+            ),
+        ),
+    ]
diff --git a/src/differential_expression/migrations/0003_alter_differentialexpressionexperiment_state.py b/src/differential_expression/migrations/0003_alter_differentialexpressionexperiment_state.py
deleted file mode 100644
index f24d56c1..00000000
--- a/src/differential_expression/migrations/0003_alter_differentialexpressionexperiment_state.py
+++ /dev/null
@@ -1,37 +0,0 @@
-# Generated by Django 4.2.19 on 2025-08-05 01:43
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        (
-            "differential_expression",
-            "0002_differentialexpressionexperiment_attempt_and_more",
-        ),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name="differentialexpressionexperiment",
-            name="state",
-            field=models.IntegerField(
-                choices=[
-                    (1, "Completed"),
-                    (2, "Finished With Error"),
-                    (3, "In Process"),
-                    (4, "Waiting For Queue"),
-                    (5, "No Samples In Common"),
-                    (6, "Stopping"),
-                    (7, "Stopped"),
-                    (8, "Reached Attempts Limit"),
-                    (9, "No Features Found"),
-                    (10, "Empty Dataset"),
-                    (11, "Timeout Exceeded"),
-                ],
-                default=4,
-                help_text="Current state of the differential expression experiment",
-            ),
-        ),
-    ]
diff --git a/src/differential_expression/migrations/0004_differentialexpressionexperiment_results_json.py b/src/differential_expression/migrations/0004_differentialexpressionexperiment_results_json.py
deleted file mode 100644
index 337e026b..00000000
--- a/src/differential_expression/migrations/0004_differentialexpressionexperiment_results_json.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# Generated by Django 4.2.19 on 2025-08-08 02:26
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        (
-            "differential_expression",
-            "0003_alter_differentialexpressionexperiment_state",
-        ),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="differentialexpressionexperiment",
-            name="results_json",
-            field=models.JSONField(
-                blank=True,
-                help_text="Complete differential expression results as JSON",
-                null=True,
-            ),
-        ),
-    ]
diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index 0c3e84d0..fd3dfadb 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -2,6 +2,196 @@
 from django.contrib.auth import get_user_model
 from institutions.models import Institution
 from django.contrib.auth.models import User
+from typing import List, Optional, Iterable
+import pandas as pd
+import numpy as np
+import math
+
+from common.constants import PATIENT_ID_COLUMN, SAMPLE_ID_COLUMN, SAMPLES_TYPE_COLUMN, PRIMARY_TYPE_VALUE
+
+class DifferentialExpressionSource(models.Model):
+    """
+    Represents a data source for differential expression experiments.
+    A source could be a user file or a CGDS Dataset.
+    """
+    user_file = models.ForeignKey(
+        'user_files.UserFile', 
+        on_delete=models.CASCADE, 
+        blank=True, 
+        null=True,
+        related_name='differential_expression_sources'
+    )
+    cgds_dataset = models.ForeignKey(
+        'datasets_synchronization.CGDSDataset', 
+        on_delete=models.CASCADE, 
+        blank=True,
+        null=True, 
+        related_name='differential_expression_sources'
+    )
+
+    def get_valid_source(self):
+        """
+        Gets the valid source depending on which has been uploaded by the user
+        @return: Valid source: a UserFile or a CGDSDataset
+        """
+        if self.user_file:
+            return self.user_file
+        elif self.cgds_dataset:
+            return self.cgds_dataset
+        else:
+            raise ValueError("No valid source found - both user_file and cgds_dataset are None")
+
+    def get_samples(self) -> List[str]:
+        """
+        Gets the samples of the source
+        @return: List with the samples
+        """
+        return self.get_valid_source().get_column_names()
+
+    def get_specific_row_and_columns(self, row: str, columns_idx: Optional[np.ndarray] = None) -> np.ndarray:
+        """
+        Gets a specific row and columns values from the source
+        @param row: Row's identifier to retrieve it
+        @param columns_idx: Indices of columns to filter, if None retrieves all the columns
+        @raise KeyError if the row data is empty
+        @return: List of values
+        """
+        row_data = self.get_valid_source().get_specific_row(row)
+        if row_data.size == 0:
+            raise KeyError(f"Row '{row}' not found in source")
+
+        if columns_idx is not None:
+            row_data = row_data[columns_idx]
+        return row_data
+
+    def get_df(self, only_matching: bool = False) -> pd.DataFrame:
+        """
+        Generates a DataFrame from the source
+        @param only_matching: If True only returns the molecules that are equal in both columns
+        @return: A DataFrame with the data to work
+        """
+        return self.get_valid_source().get_df(only_matching)
+
+    def get_df_in_chunks(self, only_matching: bool = False) -> Iterable[pd.DataFrame]:
+        """
+        Returns an Iterator of a DataFrame in divided in chunks from the source.
+        @param only_matching: If True only returns the molecules that are equal in both columns
+        @return: A DataFrame Iterator with the data to work.
+        """
+        return self.get_valid_source().get_df_in_chunks(only_matching)
+
+    @property
+    def number_of_rows(self) -> int:
+        """Number of rows in the source"""
+        return self.get_valid_source().number_of_rows
+
+    @property
+    def number_of_samples(self) -> int:
+        """Number of samples in the source"""
+        return self.get_valid_source().number_of_samples
+
+
+class DifferentialExpressionClinicalSource(DifferentialExpressionSource):
+    """
+    For clinical source of differential expression experiments. 
+    Needs an extra CGDSDataset field as cBioPortal has two clinical datasets:
+    patients data and samples data
+    """
+    extra_cgds_dataset = models.ForeignKey(
+        'datasets_synchronization.CGDSDataset',
+        on_delete=models.CASCADE, 
+        blank=True, 
+        null=True,
+        related_name='differential_expression_clinical_sources_extra'
+    )
+
+    def get_samples(self) -> List[str]:
+        """
+        Gets the samples of the clinical source
+        @return: List with the samples
+        """
+        if self.user_file:
+            # For user files, samples are in columns
+            return self.user_file.get_column_names()
+
+        # For CGDS datasets, returns a distinct concatenation of both source columns
+        # IMPORTANT: samples are in rows and attributes are in columns.
+        samples = self._get_cgds_datasets_joined_df().index
+        return list(set(samples))
+
+    def get_attributes(self) -> List[str]:
+        """
+        Gets the clinical attributes of the source without the special attributes like sample ids or patient ids
+        @return: List with the attributes
+        """
+        if self.user_file:
+            # For user files, attributes are in rows (transposed format)
+            return self.user_file.get_row_names()
+
+        # Returns a distinct concatenation of both source columns
+        columns_distinct = set()
+        if self.cgds_dataset:
+            first_clinical_source_columns = self.cgds_dataset.get_column_names()
+            columns_distinct.update(first_clinical_source_columns)
+        
+        if self.extra_cgds_dataset:
+            second_clinical_source_columns = self.extra_cgds_dataset.get_column_names()
+            columns_distinct.update(second_clinical_source_columns)
+        
+        # Remove special columns
+        special_columns = ['SAMPLE_ID', 'PATIENT_ID']
+        for column_to_remove in special_columns:
+            columns_distinct.discard(column_to_remove)
+        return list(columns_distinct)
+
+    def get_specific_samples_and_attributes(
+            self,
+            samples: Optional[List[str]],
+            clinical_attributes: List[str]
+    ) -> np.ndarray:
+        """
+        Gets specific samples and clinical attributes values from the source as a numpy array.
+        @param samples: List of samples to retrieve. If None, returns all the samples
+        @param clinical_attributes: List of clinical attributes to retrieve.
+        @return: Numpy array with values.
+        """
+        if self.user_file:
+            # For user files, use the user file's method
+            return self.user_file.get_specific_samples_and_attributes(samples, clinical_attributes)
+        else:
+            # For CGDS datasets, get the joined dataframe and filter
+            df = self._get_cgds_datasets_joined_df()
+            if samples is not None:
+                df = df.loc[samples]
+            result = df[clinical_attributes].to_numpy()
+            return result if len(clinical_attributes) > 1 else result[:, 0]
+
+    def _get_cgds_datasets_joined_df(self) -> pd.DataFrame:
+        """
+        Gets a joined DataFrame from both CGDS datasets (patient and sample data)
+        @return: Joined DataFrame
+        """
+        # This would need to be implemented based on how CGDS datasets are structured
+        # For now, return the main dataset
+        if self.cgds_dataset:
+            df1: pd.DataFrame = self.cgds_dataset.get_df(use_standard_column=False)
+            df2: pd.DataFrame = self.extra_cgds_dataset.get_df(use_standard_column=False)
+
+            # Sets the index to the patient ID column and joins both DataFrames
+            df1 = df1.reset_index().set_index([PATIENT_ID_COLUMN])
+            df2 = df2.reset_index().set_index([PATIENT_ID_COLUMN])
+
+            return df1.join(df2)
+
+    def get_df(self, only_matching: bool = False) -> pd.DataFrame:
+        """
+        Generates a DataFrame from the clinical source
+        @return: A DataFrame with the clinical data
+        """
+        if self.user_file:
+            return self.user_file.get_df()
+        else:
+            return self._get_cgds_datasets_joined_df()
 
 
 class DifferentialExpressionExperimentState(models.IntegerChoices):
@@ -28,11 +218,21 @@ class DifferentialExpressionExperiment(models.Model):
 
     # Clinical and mRNA sources
     # These are used to link the experiment to the clinical and mRNA data sources
-    clinical_source = models.ForeignKey('api_service.ExperimentClinicalSource', on_delete=models.CASCADE, null=False,
-                                        blank=False, related_name='differential_expression_as_clinical')
+    clinical_source = models.ForeignKey(
+        'DifferentialExpressionClinicalSource', 
+        on_delete=models.CASCADE, 
+        null=False,
+        blank=False, 
+        related_name='differential_expression_experiments_as_clinical'
+    )
 
-    mrna_source = models.ForeignKey('api_service.ExperimentSource', on_delete=models.CASCADE, null=False, blank=False,
-                                    related_name='differential_expression_as_mrna')
+    mrna_source = models.ForeignKey(
+        'DifferentialExpressionSource', 
+        on_delete=models.CASCADE, 
+        null=False, 
+        blank=False,
+        related_name='differential_expression_experiments_as_mrna'
+    )
 
     clinical_attribute = models.CharField(max_length=100, blank=False, null=False)
 
@@ -46,12 +246,16 @@ class DifferentialExpressionExperiment(models.Model):
     task_id = models.CharField(max_length=100, blank=True, null=True, help_text='Celery Task ID')
     attempt = models.PositiveSmallIntegerField(default=0, help_text='Number of attempts to prevent a buggy experiment '
                                                                     'running forever')
-    state : int = models.IntegerField(
+    state = models.IntegerField(
         choices=DifferentialExpressionExperimentState.choices,
         default=DifferentialExpressionExperimentState.WAITING_FOR_QUEUE,
         help_text='Current state of the differential expression experiment'
     )
     
+    # Timestamp fields
+    created_at = models.DateTimeField(auto_now_add=True, null=True, blank=True, help_text='When the experiment was created')
+    updated_at = models.DateTimeField(auto_now=True, help_text='When the experiment was last updated')
+    
     # User and sharing information
     # This is used to track the user who created the experiment and to share it with other users or institutions
     user = models.ForeignKey(get_user_model(), on_delete=models.CASCADE)
@@ -76,22 +280,43 @@ def save(self, *args, **kwargs):
 
         super().save(*args, **kwargs)
 
-
-    # Results storage
-    # Store the complete differential expression results as JSON
-    # This is more efficient than individual records for large datasets
-    results_json = models.JSONField(blank=True, null=True, help_text='Complete differential expression results as JSON')
-    
     def save_results(self, dataframe):
         """
-        Save the differential expression DataFrame results as JSON.
+        Save the differential expression DataFrame results.
         
         Args:
             dataframe: pandas DataFrame with differential expression results
         """
-        # Convert DataFrame to JSON format (records orientation)
-        self.results_json = dataframe.to_dict('records')
-        self.save(update_fields=['results_json'])
+        # Clear existing results
+        self.results.all().delete()
+        
+        # Create new result records
+        results_to_create = []
+        for gene_name, row in dataframe.iterrows():
+            # Handle NaN values by replacing them with appropriate defaults
+            def safe_float(value, default=0.0):
+                """Convert value to float, handling NaN and inf values."""
+                try:
+                    if pd.isna(value) or math.isinf(float(value)):
+                        return default
+                    return float(value)
+                except (ValueError, TypeError):
+                    return default
+            
+            result = DifferentialExpressionExperimentResult(
+                experiment=self,
+                gene=str(gene_name),  # The gene identifier from the DataFrame index
+                ave_expr=safe_float(row.get('AveExpr', 0.0), 0.0),
+                p_value=safe_float(row.get('P.Value', 1.0), 1.0),
+                adj_p_val=safe_float(row.get('adj.P.Val', 1.0), 1.0),
+                log_fc=safe_float(row.get('logFC', 0.0), 0.0),
+                t_statistic=safe_float(row.get('t', 0.0), 0.0),
+                b_statistic=safe_float(row.get('B', 0.0), 0.0)
+            )
+            results_to_create.append(result)
+        
+        # Bulk create for efficiency
+        DifferentialExpressionExperimentResult.objects.bulk_create(results_to_create)
     
     def get_results_dataframe(self):
         """
@@ -100,11 +325,26 @@ def get_results_dataframe(self):
         Returns:
             pandas.DataFrame: DataFrame with differential expression results
         """
-        if not self.results_json:
+        results = self.results.all()
+        if not results.exists():
             return None
             
         import pandas as pd
-        return pd.DataFrame(self.results_json)
+        data = []
+        for result in results:
+            data.append({
+                'gene': result.gene,
+                'AveExpr': result.ave_expr,
+                'P.Value': result.p_value,
+                'adj.P.Val': result.adj_p_val,
+                'logFC': result.log_fc,
+                't': result.t_statistic,
+                'B': result.b_statistic
+            })
+        
+        df = pd.DataFrame(data)
+        df.set_index('gene', inplace=True)
+        return df
     
     def get_significant_genes(self, p_value_threshold=0.05, log_fc_threshold=1.0):
         """
@@ -115,18 +355,48 @@ def get_significant_genes(self, p_value_threshold=0.05, log_fc_threshold=1.0):
             log_fc_threshold: Minimum absolute log fold change (default 1.0)
             
         Returns:
-            list: List of gene records meeting the criteria
+            QuerySet: QuerySet of DifferentialExpressionExperimentResult objects meeting the criteria
         """
-        if not self.results_json:
-            return []
-            
-        significant_genes = []
-        for gene in self.results_json:
-            adj_p_val = gene.get('adj.P.Val', gene.get('adjusted_p_value', 1.0))
-            log_fc = abs(gene.get('logFC', gene.get('log_fold_change', 0.0)))
-            
-            if adj_p_val <= p_value_threshold and log_fc >= log_fc_threshold:
-                significant_genes.append(gene)
-                
-        return significant_genes
+        from django.db.models import Q
+        
+        return self.results.filter(
+            Q(adj_p_val__lte=p_value_threshold) &
+            (Q(log_fc__gte=log_fc_threshold) | Q(log_fc__lte=-log_fc_threshold))
+        )
+
+
+class DifferentialExpressionExperimentResult(models.Model):
+    """
+    Model to store individual differential expression results for each gene.
+    """
+    
+    experiment = models.ForeignKey(
+        'DifferentialExpressionExperiment', 
+        on_delete=models.CASCADE, 
+        related_name='results'
+    )
+    gene = models.CharField(max_length=100, help_text='Gene identifier')
+    ave_expr = models.FloatField(help_text='Average expression level')
+    p_value = models.FloatField(help_text='P-value from statistical test')
+    adj_p_val = models.FloatField(help_text='Adjusted P-value (FDR corrected)')
+    log_fc = models.FloatField(help_text='Log fold change')
+    t_statistic = models.FloatField(help_text='t-statistic from the test')
+    b_statistic = models.FloatField(help_text='B-statistic (log-odds of differential expression)')
+    
+    class Meta:
+        unique_together = ('experiment', 'gene')
+        indexes = [
+            models.Index(fields=['experiment', 'adj_p_val']),
+            models.Index(fields=['experiment', 'log_fc']),
+            models.Index(fields=['gene']),
+        ]
+    
+    def __str__(self):
+        return f"{self.gene} - {self.experiment.name}"
+    
+    @property
+    def is_significant(self, p_threshold=0.05, fc_threshold=1.0):
+        """Check if this gene is significantly differentially expressed."""
+        return (self.adj_p_val <= p_threshold and 
+                abs(self.log_fc) >= fc_threshold)
         
\ No newline at end of file
diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index 07bc989d..a928c772 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -1,51 +1,188 @@
 from rest_framework import serializers
-
-from differential_expression.models import DifferentialExpressionExperiment
+from django.contrib.auth.models import User
+from institutions.models import Institution
+from differential_expression.models import (
+    DifferentialExpressionExperiment, 
+    DifferentialExpressionExperimentResult,
+    DifferentialExpressionSource,
+    DifferentialExpressionClinicalSource
+)
 from drf_writable_nested.serializers import WritableNestedModelSerializer
 
 
-class DifferentialExpressionExperimentSerializer(WritableNestedModelSerializer):
+class DifferentialExpressionSourceSerializer(serializers.ModelSerializer):
     """
-    Serializer for Differential Expression Experiment.
+    Serializer for Differential Expression Source.
     """
-    id = serializers.IntegerField(read_only=True)
-    name = serializers.CharField(max_length=255)
-    description = serializers.CharField(allow_blank=True, required=False)
-    user = serializers.HiddenField(
-        default=serializers.CurrentUserDefault()
-    )
-    clinical_source = serializers.CharField(max_length=255, required=False)
-    mrna_source = serializers.CharField(max_length=255, required=False)
+    source_type = serializers.SerializerMethodField()
+    source_name = serializers.SerializerMethodField()
+    file_type = serializers.SerializerMethodField()
+    
+    class Meta:
+        model = DifferentialExpressionSource
+        fields = ['id', 'source_type', 'source_name', 'file_type', 'number_of_samples', 'number_of_rows']
+        read_only_fields = ['id', 'number_of_samples', 'number_of_rows']
     
-    # Results-related fields
-    results_json = serializers.JSONField(read_only=True)
+    def get_source_type(self, obj):
+        """Returns the type of source."""
+        if obj.user_file:
+            return 'user_file'
+        elif obj.cgds_dataset:
+            return 'cgds_dataset'
+        return 'unknown'
+    
+    def get_source_name(self, obj):
+        """Returns the name of the source."""
+        try:
+            valid_source = obj.get_valid_source()
+            return getattr(valid_source, 'name', str(valid_source))
+        except:
+            return 'No source'
+    
+    def get_file_type(self, obj):
+        """Returns the file type of the source."""
+        try:
+            valid_source = obj.get_valid_source()
+            return getattr(valid_source, 'file_type', None)
+        except:
+            return None
+
+
+class DifferentialExpressionClinicalSourceSerializer(serializers.ModelSerializer):
+    """
+    Serializer for Differential Expression Clinical Source.
+    """
+    source_type = serializers.SerializerMethodField()
+    source_name = serializers.SerializerMethodField()
+    attributes_count = serializers.SerializerMethodField()
+    
+    class Meta:
+        model = DifferentialExpressionClinicalSource
+        fields = ['id', 'source_type', 'source_name', 'attributes_count', 'number_of_samples', 'number_of_rows']
+        read_only_fields = ['id', 'number_of_samples', 'number_of_rows']
+    
+    def get_source_type(self, obj):
+        """Returns the type of clinical source."""
+        if obj.user_file:
+            return 'user_file'
+        elif obj.cgds_dataset and obj.extra_cgds_dataset:
+            return 'cgds_clinical_combined'
+        elif obj.cgds_dataset:
+            return 'cgds_clinical'
+        return 'unknown'
+    
+    def get_source_name(self, obj):
+        """Returns the name of the clinical source."""
+        try:
+            if obj.user_file:
+                return obj.user_file.name
+            elif obj.cgds_dataset:
+                return obj.cgds_dataset.name
+            return 'No source'
+        except:
+            return 'No source'
+    
+    def get_attributes_count(self, obj):
+        """Returns the number of clinical attributes."""
+        try:
+            return len(obj.get_attributes())
+        except:
+            return 0
+
+
+class UserSimpleSerializer(serializers.ModelSerializer):
+    """Simple serializer for User model."""
+    class Meta:
+        model = User
+        fields = ['id', 'username', 'first_name', 'last_name', 'email']
+        read_only_fields = ['id', 'username', 'first_name', 'last_name', 'email']
+
+
+class InstitutionSimpleSerializer(serializers.ModelSerializer):
+    """Simple serializer for Institution model."""
+    class Meta:
+        model = Institution
+        fields = ['id', 'name']
+        read_only_fields = ['id', 'name']
+
+
+class DifferentialExpressionExperimentResultSerializer(serializers.ModelSerializer):
+    """
+    Serializer for Differential Expression Experiment Results.
+    """
+    is_significant = serializers.SerializerMethodField()
+    
+    class Meta:
+        model = DifferentialExpressionExperimentResult
+        fields = ['id', 'gene', 'ave_expr', 'p_value', 'adj_p_val', 'log_fc', 't_statistic', 'b_statistic', 'is_significant']
+        read_only_fields = ['id']
+    
+    def get_is_significant(self, obj):
+        """Check if this gene is significantly differentially expressed."""
+        return obj.adj_p_val <= 0.05 and abs(obj.log_fc) >= 1.0
+
+
+class DifferentialExpressionExperimentSerializer(serializers.ModelSerializer):
+    """
+    Serializer for Differential Expression Experiment (List view).
+    """
+    user = UserSimpleSerializer(read_only=True)
+    clinical_source = DifferentialExpressionClinicalSourceSerializer(read_only=True)
+    mrna_source = DifferentialExpressionSourceSerializer(read_only=True)
+    
+    # Computed fields
     has_results = serializers.SerializerMethodField()
     results_count = serializers.SerializerMethodField()
     significant_genes_count = serializers.SerializerMethodField()
-
+    state_display = serializers.CharField(source='get_state_display', read_only=True)
+    
     class Meta:
         model = DifferentialExpressionExperiment
-        fields = '__all__'
+        fields = [
+            'id', 'name', 'description', 'user', 'clinical_source', 'mrna_source',
+            'clinical_attribute', 'threshold_percentile', 'threshold', 'state', 'state_display',
+            'execution_time', 'created_at', 'updated_at', 'is_public',
+            'has_results', 'results_count', 'significant_genes_count'
+        ]
+        read_only_fields = [
+            'id', 'execution_time', 'created_at', 'updated_at', 
+            'has_results', 'results_count', 'significant_genes_count'
+        ]
     
     def get_has_results(self, obj):
         """Check if the experiment has results."""
-        return obj.results_json is not None and len(obj.results_json) > 0
+        try:
+            return obj.results.exists()
+        except:
+            return False
     
     def get_results_count(self, obj):
         """Get the total number of genes in results."""
-        if obj.results_json:
-            return len(obj.results_json)
-        return 0
+        try:
+            return obj.results.count()
+        except:
+            return 0
     
     def get_significant_genes_count(self, obj):
-        """Get the number of significant genes (adj.P.Val <= 0.05)."""
-        if not obj.results_json:
+        """Get the number of significant genes (adj.P.Val <= 0.05 and |logFC| >= 1.0)."""
+        try:
+            return obj.get_significant_genes().count()
+        except:
             return 0
-        
-        significant_count = 0
-        for gene in obj.results_json:
-            adj_p_val = gene.get('adj.P.Val', gene.get('adjusted_p_value', 1.0))
-            if adj_p_val <= 0.05:
-                significant_count += 1
-        
-        return significant_count
\ No newline at end of file
+
+
+class DifferentialExpressionExperimentDetailSerializer(DifferentialExpressionExperimentSerializer):
+    """
+    Detailed serializer for Differential Expression Experiment (Detail view).
+    Includes additional information like shared users and institutions.
+    """
+    shared_users = UserSimpleSerializer(many=True, read_only=True)
+    shared_institutions = InstitutionSimpleSerializer(many=True, read_only=True)
+    
+    class Meta(DifferentialExpressionExperimentSerializer.Meta):
+        fields = DifferentialExpressionExperimentSerializer.Meta.fields + [
+            'shared_users', 'shared_institutions', 'task_id', 'attempt'
+        ]
+        read_only_fields = DifferentialExpressionExperimentSerializer.Meta.read_only_fields + [
+            'task_id', 'attempt'
+        ]
\ No newline at end of file
diff --git a/src/differential_expression/service.py b/src/differential_expression/service.py
index 9ec50aa4..8f4a4016 100644
--- a/src/differential_expression/service.py
+++ b/src/differential_expression/service.py
@@ -1,3 +1,4 @@
+from TESTS.join_df import mrna_path
 from common.exceptions import EmptyDataset
 from differential_expression.models import DifferentialExpressionExperiment
 import pandas as pd
@@ -96,10 +97,10 @@ def perform_differential_expression(self) -> pd.DataFrame:
             # Convert the R data frame to a Pandas DataFrame for further analysis in Python.
             results_df = pandas2ri.rpy2py(results)
             
-            top_genes = results_df.nsmallest(10, 'adj.P.Val')
-            top_genes_reset = top_genes.reset_index() 
+            # Return top genes sorted by adjusted p-value, keeping gene names as index
+            top_genes = results_df.nsmallest(1000, 'adj.P.Val')
             
-            return top_genes_reset
+            return top_genes
         
         except Exception as e:
             logging.error(f"Error occurred during differential expression analysis: {e}")
@@ -187,6 +188,7 @@ def _process_clinical_data(self) -> None:
         df_clinical = df_clinical[['SAMPLE_ID', self.clinical_attribute]]
 
         df_clinical = df_clinical.drop_duplicates()
+        df_clinical['SAMPLE_ID'] = df_clinical['SAMPLE_ID'].str.replace('-', '.')
         
         self.clinical_df = df_clinical
         logging.info("Clinical data processed successfully.")
@@ -197,14 +199,39 @@ def _process_mrna_data(self) -> None:
         This method processes the mRNA dataset by renaming columns, removing duplicates,
         filtering samples based on the clinical dataset, and cleaning up NA values.
         """
-        
+
+        mrna_dataset = self.mrna_df.copy()
+
+        mrna_dataset.reset_index(inplace=True)
+
+        # SOLUCIÓN: Reemplazar guiones por puntos en los nombres de las columnas sino no puede machear con SAMPLE_ID
+        columns_to_rename = {}
+        for col in mrna_dataset.columns:
+            if col not in 'Standard_Symbol':
+                columns_to_rename[col] = col.replace('-', '.')
+
+        mrna_dataset = mrna_dataset.rename(columns=columns_to_rename)
+
+        mrna_dataset = mrna_dataset.drop_duplicates(subset=['Standard_Symbol'], keep='first')
+
+        # # Si Standard_Symbol está como índice, convertirlo a columna
+        # if mrna_dataset.index.name == 'Standard_Symbol' in str(mrna_dataset.index.name):
+        #     mrna_dataset = mrna_dataset.reset_index()
+
+        # Si Standard_Symbol no está como columna pero está en el índice
+        # if 'Standard_Symbol' not in mrna_dataset.columns and mrna_dataset.index.name is not None:
+        #     mrna_dataset = mrna_dataset.reset_index()
+        #     # Renombrar la primera columna a Standard_Symbol si es necesario
+        #     if mrna_dataset.columns[0] != 'Standard_Symbol':
+        #         mrna_dataset = mrna_dataset.rename(columns={mrna_dataset.columns[0]: 'Standard_Symbol'})
+
 
         # Eliminar duplicados manteniendo la primera ocurrencia
-        mrna_dataset = self.mrna_df.drop_duplicates(subset=['Standard_Symbol'], keep='first')
+        # mrna_dataset = self.mrna_df.drop_duplicates(subset=['Standard_Symbol'], keep='first')
         
         # Antes de la intersección, normalizar los SAMPLE_ID extrayendo solo la parte base
-        self.clinical_df['SAMPLE_ID'] = self.clinical_df['SAMPLE_ID'].str.rsplit('-', n=1).str[0]
-        
+        self.clinical_df['SAMPLE_ID'] = self.clinical_df['SAMPLE_ID'].str.rsplit('.', n=1).str[0]
+
         # Obtener valores de SAMPLE_ID del DataFrame de metadatos
         valid_columns = list(set(mrna_dataset.columns) & set(self.clinical_df['SAMPLE_ID']))
         
diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index 7c36fc43..5c2a34ac 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -4,5 +4,7 @@
 urlpatterns = [
     path('', views.DifferentialExpressionList.as_view(), name='differential_expression_list'),
     path('<int:pk>/', views.DifferentialExpressionDetail.as_view()),
+    path('<int:pk>/results/', views.DifferentialExpressionResults.as_view()),
+    path('<int:pk>/significant-genes/', views.DifferentialExpressionSignificantGenes.as_view()),
     path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
 ]
\ No newline at end of file
diff --git a/src/differential_expression/utils.py b/src/differential_expression/utils.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 65c4bdaf..68b9262e 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -1,23 +1,99 @@
-from django.shortcuts import render
 from django.db import transaction
 from rest_framework.request import Request
 from rest_framework.views import APIView
-from common.utils import get_source_pk
-from api_service.utils import get_experiment_source
+from api_service.enums import SourceType
+from api_service.utils import get_cgds_dataset
+from datasets_synchronization.models import CGDSStudy
+from user_files.models import UserFile
 from user_files.models_choices import FileType
+from user_files.views import get_an_user_file
 from rest_framework.exceptions import ValidationError
-from differential_expression.models import DifferentialExpressionExperiment
+from differential_expression.models import (
+    DifferentialExpressionExperiment, 
+    DifferentialExpressionSource,
+    DifferentialExpressionClinicalSource
+)
 from rest_framework.response import Response
-from rest_framework import generics, permissions, filters, status
+from rest_framework import generics, permissions, filters
 from rest_framework.generics import get_object_or_404
-from django.db.models import QuerySet, Q
-from differential_expression.serializers import DifferentialExpressionExperimentSerializer
+from django.db.models import Q
+from differential_expression.serializers import (
+    DifferentialExpressionExperimentSerializer, 
+    DifferentialExpressionExperimentDetailSerializer,
+    DifferentialExpressionExperimentResultSerializer
+)
 from django_filters.rest_framework import DjangoFilterBackend
 from common.pagination import StandardResultsSetPagination
-from celery.contrib.abortable import AbortableAsyncResult
 from .tasks import eval_differential_expression_experiment
 
 
+def create_differential_expression_source(
+    source_type: int,
+    request: Request,
+    file_type: FileType,
+    prefix: str
+) -> tuple[DifferentialExpressionSource | DifferentialExpressionClinicalSource | None, DifferentialExpressionClinicalSource | None]:
+    """
+    Creates a Source object for differential expression experiments.
+    """
+    is_clinical = prefix == 'clinical'
+    source = DifferentialExpressionClinicalSource() if is_clinical else DifferentialExpressionSource()
+    clinical_source = None
+    
+    if source_type == SourceType.NEW_DATASET.value:
+        # Adds a new User's file and uses it
+        source_file = getattr(request, 'FILES', {}).get(f'{prefix}File')
+        if source_file is None:
+            return None, None
+
+        user_file = UserFile(
+            name=source_file.name,
+            description=None,
+            file_obj=source_file,
+            file_type=file_type,
+            user=request.user
+        )
+        user_file.save()
+        user_file.compute_post_saved_field()
+        source.user_file = user_file
+        
+    elif source_type == SourceType.CGDS.value:
+        # Gets the CGDS Study
+        post_data = getattr(request, 'data', {}) or getattr(request, 'POST', {})
+        cgds_study_pk = post_data.get(f'{prefix}CGDSStudyPk')
+        if not cgds_study_pk:
+            return None, None
+            
+        cgds_study = CGDSStudy.objects.get(pk=int(cgds_study_pk))
+        
+        if is_clinical:
+            # For clinical sources, we need both datasets
+            if cgds_study.clinical_patient_dataset and cgds_study.clinical_sample_dataset:
+                source.cgds_dataset = cgds_study.clinical_patient_dataset
+                source.extra_cgds_dataset = cgds_study.clinical_sample_dataset
+            else:
+                return None, None
+        else:
+            cgds_dataset = get_cgds_dataset(cgds_study, file_type)
+            if cgds_dataset:
+                source.cgds_dataset = cgds_dataset
+            else:
+                return None, None
+        
+    else:
+        # Uses an existing User's file
+        post_data = getattr(request, 'data', {}) or getattr(request, 'POST', {})
+        existing_file_pk = post_data.get(f'{prefix}ExistingFilePk')
+        if not existing_file_pk:
+            return None, None
+            
+        user_file = get_an_user_file(user=request.user, user_file_pk=int(existing_file_pk))
+        source.user_file = user_file
+
+    source.save()
+    return source, clinical_source
+
+
 class DifferentialExpressionDetail(generics.RetrieveAPIView):
     """
     Endpoint to retrieve a differential expression experiment.
@@ -38,13 +114,12 @@ def get_object(self) -> DifferentialExpressionExperiment:
                 experiment.shared_users.filter(id=user.id).exists()):
             raise ValidationError('You do not have permission to access this experiment.')
 
-        print(experiment.clinical_source.get_attributes())
-
         return experiment
 
-    serializer_class = DifferentialExpressionExperimentSerializer
+    serializer_class = DifferentialExpressionExperimentDetailSerializer
     permission_classes = [permissions.IsAuthenticated]
 
+
 class DifferentialExpressionList(generics.ListAPIView):
     """
     Endpoint to list all differential expression experiments.
@@ -76,57 +151,68 @@ class DifferentialExpressionSubmit(APIView):
     Endpoint to submit a differential expression experiment.
     """
 
-    def post(self, request : Request):
+    def post(self, request: Request):
         """
         Endpoint to submit a differential expression experiment.
         """
         with transaction.atomic():
-
-            name = request.POST.get('name', 'Differential Expression Experiment')
-            description = request.POST.get('description', '')
+            # Get basic experiment data
+            post_data = getattr(request, 'data', {}) or getattr(request, 'POST', {})
+            
+            name = post_data.get('name', 'Differential Expression Experiment')
+            description = post_data.get('description', '')
 
             # Clinical source
-            clinical_source_type = get_source_pk(request.POST, 'clinicalType')
-            clinical_source, clinical_aux = get_experiment_source(clinical_source_type, request, FileType.CLINICAL,
-                                                                  'clinical')
-
-            # Select the valid one (if it's a CGDSStudy it needs clinical_aux as it has both needed CGDSDatasets)
-            clinical_source = clinical_aux if clinical_aux is not None else clinical_source
+            clinical_source_type = post_data.get('clinicalType')
+            if clinical_source_type:
+                clinical_source_type = int(clinical_source_type)
+                clinical_source, clinical_aux = create_differential_expression_source(
+                    clinical_source_type, request, FileType.CLINICAL, 'clinical')
+                # Select the valid one (if it's a CGDSStudy it needs clinical_aux as it has both needed CGDSDatasets)
+                clinical_source = clinical_aux if clinical_aux is not None else clinical_source
+            else:
+                clinical_source = None
 
             if clinical_source is None:
                 raise ValidationError('Invalid clinical source')
 
             # mRNA source
-            mrna_source_type = get_source_pk(request.POST, 'mRNAType')
-            mrna_source, _mrna_clinical = get_experiment_source(mrna_source_type, request, FileType.MRNA, 'mRNA')
+            mrna_source_type = post_data.get('mRNAType')
+            if mrna_source_type:
+                mrna_source_type = int(mrna_source_type)
+                mrna_source, _mrna_clinical = create_differential_expression_source(
+                    mrna_source_type, request, FileType.MRNA, 'mRNA')
+            else:
+                mrna_source = None
 
             if mrna_source is None:
                 raise ValidationError('Invalid mRNA source')
 
             # Clinical attribute
-            clinical_attribute = request.POST.get('clinicalAttribute', None)
+            clinical_attribute = post_data.get('clinicalAttribute')
             if not clinical_attribute:
                 raise ValidationError('Clinical attribute is required')
 
             # Threshold percentile
             try:
-                threshold_percentile = float(request.POST.get('thresholdPercentile', 0.15))
-            except ValueError:
-                raise ValidationError('Invalid threshold percentile value')
+                threshold_percentile_str = post_data.get('thresholdPercentile', '0.15')
+                threshold_percentile = float(threshold_percentile_str)
+            except (ValueError, TypeError) as exc:
+                raise ValidationError('Invalid threshold percentile value') from exc
 
             if threshold_percentile < 0 or threshold_percentile > 1:
                 raise ValidationError('Threshold percentile must be between 0 and 1')
 
             # Threshold
             try:
-                threshold = float(request.POST.get('threshold', 0.0001))
-            except ValueError:
-                raise ValidationError('Invalid threshold value')
+                threshold_str = post_data.get('threshold', '0.0001')
+                threshold = float(threshold_str)
+            except (ValueError, TypeError) as exc:
+                raise ValidationError('Invalid threshold value') from exc
 
             if threshold < 0 or threshold > 1:
                 raise ValidationError('Threshold must be between 0 and 1')
 
-
             # Create the differential expression experiment
             experiment = DifferentialExpressionExperiment.objects.create(
                 name=name,
@@ -136,20 +222,79 @@ def post(self, request : Request):
                 clinical_attribute=clinical_attribute,
                 threshold_percentile=threshold_percentile,
                 threshold=threshold,
-                user = request.user,
+                user=request.user,
             )
 
-            # async_res: AbortableAsyncResult = eval_feature_selection_experiment.apply_async(
-            # (fs_experiment.pk, fit_fun_enum, fitness_function_parameters, algorithm_parameters,
-            #  cross_validation_parameters), queue='feature_selection')
-
-            # fs_experiment.task_id = async_res.task_id
-            # fs_experiment.save(update_fields=['task_id'])
-            
-            async_res : AbortableAsyncResult = eval_differential_expression_experiment.apply_async(
+            # Start the async task
+            async_res = eval_differential_expression_experiment.apply_async(
                 (experiment.pk,), queue='differential_expression')
             
             experiment.task_id = async_res.task_id
             experiment.save(update_fields=['task_id'])
 
             return Response({'ok': True})
+
+
+class DifferentialExpressionResults(generics.ListAPIView):
+    """
+    Endpoint to get all results for a differential expression experiment.
+    """
+    serializer_class = DifferentialExpressionExperimentResultSerializer
+    permission_classes = [permissions.IsAuthenticated]
+    pagination_class = StandardResultsSetPagination
+    filter_backends = [filters.OrderingFilter, DjangoFilterBackend]
+    ordering_fields = ['adj_p_val', 'log_fc', 'p_value', 'ave_expr']
+    ordering = ['adj_p_val']  # Default ordering by adjusted p-value
+    
+    def get_queryset(self):
+        experiment_id = self.kwargs.get('pk')
+        experiment = get_object_or_404(DifferentialExpressionExperiment, pk=experiment_id)
+        
+        # Check permissions
+        user = self.request.user
+        if not (experiment.is_public or
+                experiment.user == user or
+                experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
+                experiment.shared_users.filter(id=user.id).exists()):
+            raise ValidationError('You do not have permission to access this experiment.')
+        
+        return experiment.results.all()
+
+
+class DifferentialExpressionSignificantGenes(generics.ListAPIView):
+    """
+    Endpoint to get significant genes for a differential expression experiment.
+    """
+    serializer_class = DifferentialExpressionExperimentResultSerializer
+    permission_classes = [permissions.IsAuthenticated]
+    pagination_class = StandardResultsSetPagination
+    filter_backends = [filters.OrderingFilter]
+    ordering_fields = ['adj_p_val', 'log_fc', 'p_value', 'ave_expr']
+    ordering = ['adj_p_val']  # Default ordering by adjusted p-value
+    
+    def get_queryset(self):
+        experiment_id = self.kwargs.get('pk')
+        experiment = get_object_or_404(DifferentialExpressionExperiment, pk=experiment_id)
+        
+        # Check permissions (same logic as DifferentialExpressionDetail)
+        user = self.request.user
+        if not (experiment.is_public or
+                experiment.user == user or
+                experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
+                experiment.shared_users.filter(id=user.id).exists()):
+            raise ValidationError('You do not have permission to access this experiment.')
+        
+        # Get query parameters for filtering
+        try:
+            p_threshold = float(self.request.query_params.get('p_threshold', 0.05))
+            fc_threshold = float(self.request.query_params.get('fc_threshold', 2.0))
+        except ValueError as exc:
+            raise ValidationError('Invalid threshold values. Must be numeric.') from exc
+        
+        # Validate thresholds
+        if p_threshold < 0 or p_threshold > 1:
+            raise ValidationError('p_threshold must be between 0 and 1')
+        if fc_threshold < 0:
+            raise ValidationError('fc_threshold must be positive')
+        
+        return experiment.get_significant_genes(p_threshold, fc_threshold)
diff --git a/src/frontend/templates/frontend/differential-expression.html b/src/frontend/templates/frontend/differential-expression.html
index 0065ea46..930b49d8 100644
--- a/src/frontend/templates/frontend/differential-expression.html
+++ b/src/frontend/templates/frontend/differential-expression.html
@@ -3,7 +3,7 @@
 {% load render_bundle from webpack_loader %}
 
 {% block title %}| Differential expression experiments{% endblock %}
-{% block meta_description %}Todo: cambiar Description.{% endblock %}
+{% block meta_description %}Perform differential expression analysis to identify genes with significantly different expression levels between conditions. Configure experiments, analyze results, and discover biomarkers for your research.{% endblock %}
 
 {% block css %}
         {% render_bundle 'differentialExpression' 'css' %}
@@ -15,6 +15,26 @@
 
 {% block js %}
         <script>
+            const urlDifferentialExpressionList = "{% url 'differential_expression_list' %}"
+            const urlDifferentialExpressionSubmit = "{% url 'differential_expression_submit' %}"
+            const downloadFileURL = "{% url 'download_user_file' %}"
+            const urlGetUsersCandidatesLimited = "{% url 'user_candidates_limited_institution' %}"
+            const urlGetInstitutionsNonInExperiment = "{% url 'institution-non-experiments-list' %}"
+            const urlGetUsersNonInExperiment = "{% url 'user-non-experiments-list' %}"
+            const urlShareExperimentToInstitution = "{% url 'share-experiment-to-institution' %}"
+            const urlShareExperimentToUser = "{% url 'share-experiment-to-user' %}"
+            const urlGetSharedInstitution = "{% url 'shared-institution' %}"
+            const urlGetSharedUsers = "{% url 'shared-users' %}"
+            const urlPostSwitchInstitutionPublicView = "{% url 'switch-experiment-public-view' %}"
+            const urlPostRemoveInstitution = "{% url 'remove-institution' %}"
+            const urlPostRemoveUser = "{% url 'remove-user' %}"
+            const urlGetCommonSamples = "{% url 'get_number_samples_in_common' %}"
+            const urlGetCommonSamplesClinical = "{% url 'get_number_samples_in_common_clinical_validation' %}"
+            const urlGetCommonSamplesClinicalSource = "{% url 'get_number_samples_in_common_clinical_validation_source' %}"
+            const urlGetCommonSamplesOneFront = "{% url 'get_number_samples_in_common_one_front' %}"
+            const urlUnlinkClinicalSourceUserFile = "{% url 'unlink_clinical_source_user_file' %}"
+            const maximumNumberOfOpenTabs = Number.parseInt("{{ maximum_number_of_open_tabs }}")
+            const thresholdToConsiderOrdinal = Number.parseInt("{{ threshold_to_consider_ordinal }}")
         </script>
         {% render_bundle 'differentialExpression' 'js' %}
 {% endblock %}
\ No newline at end of file
diff --git a/src/frontend/views.py b/src/frontend/views.py
index 3a402345..7243b6c3 100644
--- a/src/frontend/views.py
+++ b/src/frontend/views.py
@@ -50,7 +50,14 @@ def biomarker(request):
 @login_required
 def differential_expression(request):
     """Differential expression experiment view"""
-    return render(request, "frontend/differential-expression.html")
+    return render(
+        request,
+        "frontend/differential-expression.html",
+        {
+            'maximum_number_of_open_tabs': settings.MAX_NUMBER_OF_OPEN_TABS,
+            'threshold_to_consider_ordinal': settings.THRESHOLD_ORDINAL
+        }
+    )
 
 
 def open_source(request):

From 1a754ba43bb7016623c9772caa1e9118b4b9bc77 Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Thu, 14 Aug 2025 00:49:19 -0300
Subject: [PATCH 07/47] Add 'top' parameter to differential expression
 experiments

Introduces a 'top' field to DifferentialExpressionExperiment to control the number of significant results returned (max 1000). Updates model, admin, serializer, view, and service logic to support this parameter, adds validation, and improves error handling for cases with no samples or features. Also updates frontend template metadata and page title.
---
 config/requirements.txt                       |  1 +
 config/requirements_celery.txt                |  1 +
 src/differential_expression/admin.py          |  4 +-
 ...entialexpressionexperiment_top_and_more.py | 33 +++++++++++++++
 src/differential_expression/models.py         | 14 ++++---
 src/differential_expression/serializers.py    | 18 +++++---
 src/differential_expression/service.py        | 42 +++++++++++++++----
 src/differential_expression/tasks.py          | 41 ++++++++++++++++--
 src/differential_expression/views.py          | 42 ++++++++++++-------
 .../frontend/differential-expression.html     | 22 +---------
 10 files changed, 158 insertions(+), 60 deletions(-)
 create mode 100644 src/differential_expression/migrations/0003_differentialexpressionexperiment_top_and_more.py

diff --git a/config/requirements.txt b/config/requirements.txt
index 253e7564..223b75ca 100644
--- a/config/requirements.txt
+++ b/config/requirements.txt
@@ -28,3 +28,4 @@ scipy==1.13.0
 statsmodels==0.14.2
 xlrd==2.0.1
 openpyxl==3.1.5
+rpy2==3.6.1
\ No newline at end of file
diff --git a/config/requirements_celery.txt b/config/requirements_celery.txt
index 859c0823..c69a236b 100644
--- a/config/requirements_celery.txt
+++ b/config/requirements_celery.txt
@@ -25,3 +25,4 @@ scipy==1.13.0
 statsmodels==0.14.2
 xlrd==2.0.1
 openpyxl==3.1.5
+rpy2==3.6.1
\ No newline at end of file
diff --git a/src/differential_expression/admin.py b/src/differential_expression/admin.py
index 4a6ec737..7ace471f 100644
--- a/src/differential_expression/admin.py
+++ b/src/differential_expression/admin.py
@@ -102,7 +102,7 @@ class DifferentialExpressionExperimentAdmin(admin.ModelAdmin):
     
     list_display = (
         'id', 'name', 'user', 'state', 'clinical_attribute', 
-        'threshold_percentile', 'threshold', 'execution_time', 'created_at'
+        'threshold_percentile', 'threshold', 'top', 'execution_time', 'created_at'
     )
     list_filter = (
         'state', 'is_public', 'clinical_attribute', 'created_at'
@@ -122,7 +122,7 @@ class DifferentialExpressionExperimentAdmin(admin.ModelAdmin):
             'fields': ('clinical_source', 'mrna_source')
         }),
         ('Analysis Parameters', {
-            'fields': ('clinical_attribute', 'threshold_percentile', 'threshold')
+            'fields': ('clinical_attribute', 'threshold_percentile', 'threshold', 'top')
         }),
         ('Execution Information', {
             'fields': ('state', 'task_id', 'execution_time', 'attempt', 'created_at', 'updated_at'),
diff --git a/src/differential_expression/migrations/0003_differentialexpressionexperiment_top_and_more.py b/src/differential_expression/migrations/0003_differentialexpressionexperiment_top_and_more.py
new file mode 100644
index 00000000..918ccde1
--- /dev/null
+++ b/src/differential_expression/migrations/0003_differentialexpressionexperiment_top_and_more.py
@@ -0,0 +1,33 @@
+# Generated by Django 4.2.19 on 2025-08-14 02:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "differential_expression",
+            "0002_differentialexpressionexperiment_created_at_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="differentialexpressionexperiment",
+            name="top",
+            field=models.IntegerField(
+                default=100,
+                help_text="Number of significant results to keep (max 1000)",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="differentialexpressionexperiment",
+            name="created_at",
+            field=models.DateTimeField(
+                auto_now_add=True,
+                help_text="When the experiment was created",
+                null=True,
+            ),
+        ),
+    ]
diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index fd3dfadb..2439a57e 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -7,7 +7,7 @@
 import numpy as np
 import math
 
-from common.constants import PATIENT_ID_COLUMN, SAMPLE_ID_COLUMN, SAMPLES_TYPE_COLUMN, PRIMARY_TYPE_VALUE
+from common.constants import PATIENT_ID_COLUMN
 
 class DifferentialExpressionSource(models.Model):
     """
@@ -240,6 +240,13 @@ class DifferentialExpressionExperiment(models.Model):
 
     threshold = models.FloatField(default=0.0001, blank=False, null=False)
 
+    top = models.IntegerField(
+        default=100, 
+        blank=False, 
+        null=False,
+        help_text='Number of significant results to keep (max 1000)'
+    )
+
     # Celery task related fields
     # This is used to track the execution of the task and its state
     execution_time = models.FloatField(default=0.0, blank=True, null=True, help_text='Execution time in seconds')
@@ -321,15 +328,11 @@ def safe_float(value, default=0.0):
     def get_results_dataframe(self):
         """
         Retrieve results as a pandas DataFrame.
-        
-        Returns:
-            pandas.DataFrame: DataFrame with differential expression results
         """
         results = self.results.all()
         if not results.exists():
             return None
             
-        import pandas as pd
         data = []
         for result in results:
             data.append({
@@ -399,4 +402,3 @@ def is_significant(self, p_threshold=0.05, fc_threshold=1.0):
         """Check if this gene is significantly differentially expressed."""
         return (self.adj_p_val <= p_threshold and 
                 abs(self.log_fc) >= fc_threshold)
-        
\ No newline at end of file
diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index a928c772..1d9ec685 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -7,7 +7,6 @@
     DifferentialExpressionSource,
     DifferentialExpressionClinicalSource
 )
-from drf_writable_nested.serializers import WritableNestedModelSerializer
 
 
 class DifferentialExpressionSourceSerializer(serializers.ModelSerializer):
@@ -76,10 +75,18 @@ def get_source_name(self, obj):
         try:
             if obj.user_file:
                 return obj.user_file.name
+            elif obj.cgds_dataset and obj.extra_cgds_dataset:
+                # For combined CGDS clinical sources, show both dataset names
+                main_name = str(obj.cgds_dataset)
+                extra_name = str(obj.extra_cgds_dataset)
+                return f"Clinical Combined: {main_name} + {extra_name}"
             elif obj.cgds_dataset:
-                return obj.cgds_dataset.name
+                return str(obj.cgds_dataset)
             return 'No source'
-        except:
+        except Exception as e:
+            # More detailed error logging for debugging
+            import logging
+            logging.error(f"Error getting clinical source name: {e}")
             return 'No source'
     
     def get_attributes_count(self, obj):
@@ -114,7 +121,8 @@ class DifferentialExpressionExperimentResultSerializer(serializers.ModelSerializ
     
     class Meta:
         model = DifferentialExpressionExperimentResult
-        fields = ['id', 'gene', 'ave_expr', 'p_value', 'adj_p_val', 'log_fc', 't_statistic', 'b_statistic', 'is_significant']
+        fields = ['id', 'gene', 'ave_expr', 'p_value', 'adj_p_val', 'log_fc', 't_statistic', 'b_statistic', 'is_significant'
+        ]
         read_only_fields = ['id']
     
     def get_is_significant(self, obj):
@@ -140,7 +148,7 @@ class Meta:
         model = DifferentialExpressionExperiment
         fields = [
             'id', 'name', 'description', 'user', 'clinical_source', 'mrna_source',
-            'clinical_attribute', 'threshold_percentile', 'threshold', 'state', 'state_display',
+            'clinical_attribute', 'threshold_percentile', 'threshold', 'top', 'state', 'state_display',
             'execution_time', 'created_at', 'updated_at', 'is_public',
             'has_results', 'results_count', 'significant_genes_count'
         ]
diff --git a/src/differential_expression/service.py b/src/differential_expression/service.py
index 8f4a4016..79687c4a 100644
--- a/src/differential_expression/service.py
+++ b/src/differential_expression/service.py
@@ -1,17 +1,26 @@
-from TESTS.join_df import mrna_path
 from common.exceptions import EmptyDataset
+from common.typing import AbortEvent
 from differential_expression.models import DifferentialExpressionExperiment
-import pandas as pd
-import numpy as np
 import logging
-from common.typing import AbortEvent
-    
+import warnings
+from itertools import combinations
+
+import numpy as np
+import pandas as pd
+
+# Filter R warnings BEFORE importing rpy2
+warnings.filterwarnings('ignore',
+                       message='Environment variable "XPC_SERVICE_NAME" redefined by R',
+                       category=UserWarning)
+warnings.filterwarnings('ignore',
+                       message='Environment variable "R_SESSION_TMPDIR" redefined by R and overriding existing variable.',
+                       category=UserWarning)
+
 import rpy2.robjects as robjects
+from rpy2.robjects import pandas2ri
 from rpy2.robjects.conversion import get_conversion, localconverter
 from rpy2.robjects.pandas2ri import converter
-from rpy2.robjects import pandas2ri
 from rpy2.robjects.packages import importr
-from itertools import combinations
 
 class DifferentialExpressionService:
     def __init__(self, experiment: DifferentialExpressionExperiment, is_aborted: AbortEvent):
@@ -24,19 +33,29 @@ def perform_differential_expression(self) -> pd.DataFrame:
         sample_column = 'SAMPLE_ID'
         if sample_column in clinical_df.columns:
             common_samples = sorted(set(mrna_df.columns) & set(clinical_df[sample_column]))
+
+            # Check if there are samples in common
+            if len(common_samples) == 0:
+                from differential_expression.models import DifferentialExpressionExperimentState
+                raise ValueError("NO_SAMPLES_IN_COMMON")
+
             df_RNAseq_filtered = mrna_df[common_samples]
             df_clinical_filtered = clinical_df[clinical_df[sample_column].isin(common_samples)]
             df_clinical_filtered = df_clinical_filtered.set_index(sample_column).reindex(common_samples).reset_index()
         else:
             df_RNAseq_filtered = mrna_df
             df_clinical_filtered = clinical_df
+
+        # Check if we have any features (genes) left after filtering
+        if df_RNAseq_filtered.empty or df_RNAseq_filtered.shape[0] == 0:
+            raise ValueError("NO_FEATURES_FOUND")
             
         try:
             # Import R packages
             limma = importr('limma')  # limma for differential expression
             stats = importr('stats')  # stats for model matrix
             base = importr('base')  # base R functions
-            
+
             # 1. Validation: Ensure the clinical attribute has at least two categories
             # This is necessary because differential expression requires at least two groups to compare.
             unique_values = df_clinical_filtered[self.experiment.clinical_attribute].dropna().unique()
@@ -98,7 +117,7 @@ def perform_differential_expression(self) -> pd.DataFrame:
             results_df = pandas2ri.rpy2py(results)
             
             # Return top genes sorted by adjusted p-value, keeping gene names as index
-            top_genes = results_df.nsmallest(1000, 'adj.P.Val')
+            top_genes = results_df.nsmallest(self.experiment.top, 'adj.P.Val')
             
             return top_genes
         
@@ -300,6 +319,11 @@ def _filter_genes_by_variance(self) -> None:
         # Filter out genes with variance below the threshold
         genes_to_keep = variances > self.threshold
         self.mrna_df = self.mrna_df[genes_to_keep]
+
+        # Check if we still have features after filtering
+        if self.mrna_df.empty or self.mrna_df.shape[0] == 0:
+            raise ValueError("NO_FEATURES_FOUND")
+
         logging.info(f"Filtered genes by variance. Threshold: {self.threshold:.2f}")
         
     
diff --git a/src/differential_expression/tasks.py b/src/differential_expression/tasks.py
index d99d2bd3..5359e837 100644
--- a/src/differential_expression/tasks.py
+++ b/src/differential_expression/tasks.py
@@ -1,12 +1,16 @@
 import logging
 import time
+
 from celery.contrib.abortable import AbortableTask
-from multiomics_intermediate.celery import app
+from celery.exceptions import SoftTimeLimitExceeded
 from django.conf import settings
-from api_service import models as api_models
-from time import sleep
-from differential_expression.models import DifferentialExpressionExperiment, DifferentialExpressionExperimentState
+from multiomics_intermediate.celery import app
+
 from common.exceptions import EmptyDataset, ExperimentStopped
+from differential_expression.models import (
+    DifferentialExpressionExperiment,
+    DifferentialExpressionExperimentState,
+)
 from .service import DifferentialExpressionService
 
 @app.task(bind=True, base=AbortableTask, acks_late=True, reject_on_worker_lost=True,
@@ -50,6 +54,8 @@ def eval_differential_expression_experiment(self, experiment_pk: int, ):
         
         # If user cancel the experiment, discard changes
         if self.is_aborted():
+            experiment.state = DifferentialExpressionExperimentState.STOPPING
+            experiment.save(update_fields=['state'])
             raise ExperimentStopped
         
         # Save the results to the database if we got results
@@ -69,6 +75,33 @@ def eval_differential_expression_experiment(self, experiment_pk: int, ):
         experiment.save(update_fields=['state'])
         return
 
+    except SoftTimeLimitExceeded as e:
+        # If celery soft time limit is exceeded, sets the experiment as TIMEOUT_EXCEEDED
+        logging.warning(f'DifferentialExpressionExperiment {experiment.pk} has exceeded the soft time limit')
+        logging.exception(e)
+        experiment.state = DifferentialExpressionExperimentState.TIMEOUT_EXCEEDED
+        experiment.save(update_fields=['state'])
+        return
+
+    except ValueError as e:
+        error_msg = str(e)
+        if error_msg == "NO_SAMPLES_IN_COMMON":
+            logging.error(f'No samples in common for DifferentialExpressionExperiment {experiment.pk}')
+            experiment.state = DifferentialExpressionExperimentState.NO_SAMPLES_IN_COMMON
+            experiment.save(update_fields=['state'])
+            return
+        elif error_msg == "NO_FEATURES_FOUND":
+            logging.error(f'No features found after filtering for DifferentialExpressionExperiment {experiment.pk}')
+            experiment.state = DifferentialExpressionExperimentState.NO_FEATURES_FOUND
+            experiment.save(update_fields=['state'])
+            return
+        else:
+            # Handle other ValueError cases
+            logging.error(f'ValueError during evaluation of DifferentialExperimentExperiment {experiment.pk}: {e}')
+            experiment.state = DifferentialExpressionExperimentState.FINISHED_WITH_ERROR
+            experiment.save(update_fields=['state'])
+            raise e
+
     except Exception as e:
         logging.error(f'Error during evaluation of DifferentialExpressionExperiment {experiment.pk}: {e}')
         experiment.state = DifferentialExpressionExperimentState.FINISHED_WITH_ERROR
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 68b9262e..c41b29a3 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -1,29 +1,32 @@
 from django.db import transaction
+from django.db.models import Q
+
+from django_filters.rest_framework import DjangoFilterBackend
+from rest_framework import filters, generics, permissions
+from rest_framework.exceptions import ValidationError
+from rest_framework.generics import get_object_or_404
 from rest_framework.request import Request
+from rest_framework.response import Response
 from rest_framework.views import APIView
+
 from api_service.enums import SourceType
 from api_service.utils import get_cgds_dataset
+from common.pagination import StandardResultsSetPagination
 from datasets_synchronization.models import CGDSStudy
-from user_files.models import UserFile
-from user_files.models_choices import FileType
-from user_files.views import get_an_user_file
-from rest_framework.exceptions import ValidationError
 from differential_expression.models import (
-    DifferentialExpressionExperiment, 
+    DifferentialExpressionClinicalSource,
+    DifferentialExpressionExperiment,
     DifferentialExpressionSource,
-    DifferentialExpressionClinicalSource
 )
-from rest_framework.response import Response
-from rest_framework import generics, permissions, filters
-from rest_framework.generics import get_object_or_404
-from django.db.models import Q
 from differential_expression.serializers import (
-    DifferentialExpressionExperimentSerializer, 
     DifferentialExpressionExperimentDetailSerializer,
-    DifferentialExpressionExperimentResultSerializer
+    DifferentialExpressionExperimentResultSerializer,
+    DifferentialExpressionExperimentSerializer,
 )
-from django_filters.rest_framework import DjangoFilterBackend
-from common.pagination import StandardResultsSetPagination
+from user_files.models import UserFile
+from user_files.models_choices import FileType
+from user_files.views import get_an_user_file
+
 from .tasks import eval_differential_expression_experiment
 
 
@@ -213,6 +216,16 @@ def post(self, request: Request):
             if threshold < 0 or threshold > 1:
                 raise ValidationError('Threshold must be between 0 and 1')
 
+            # Top parameter
+            try:
+                top_str = post_data.get('top', '100')
+                top = int(top_str)
+            except (ValueError, TypeError) as exc:
+                raise ValidationError('Invalid top value') from exc
+
+            if top < 1 or top > 1000:
+                raise ValidationError('Top must be between 1 and 1000')
+
             # Create the differential expression experiment
             experiment = DifferentialExpressionExperiment.objects.create(
                 name=name,
@@ -222,6 +235,7 @@ def post(self, request: Request):
                 clinical_attribute=clinical_attribute,
                 threshold_percentile=threshold_percentile,
                 threshold=threshold,
+                top=top,
                 user=request.user,
             )
 
diff --git a/src/frontend/templates/frontend/differential-expression.html b/src/frontend/templates/frontend/differential-expression.html
index 930b49d8..eb7f198e 100644
--- a/src/frontend/templates/frontend/differential-expression.html
+++ b/src/frontend/templates/frontend/differential-expression.html
@@ -2,8 +2,8 @@
 {% load static %}
 {% load render_bundle from webpack_loader %}
 
-{% block title %}| Differential expression experiments{% endblock %}
-{% block meta_description %}Perform differential expression analysis to identify genes with significantly different expression levels between conditions. Configure experiments, analyze results, and discover biomarkers for your research.{% endblock %}
+{% block title %}| Differential Expression{% endblock %}
+{% block meta_description %}Perform differential gene expression analysis to identify significantly expressed genes between different conditions. Configure parameters, visualize results, and export comprehensive reports for your research.{% endblock %}
 
 {% block css %}
         {% render_bundle 'differentialExpression' 'css' %}
@@ -17,24 +17,6 @@
         <script>
             const urlDifferentialExpressionList = "{% url 'differential_expression_list' %}"
             const urlDifferentialExpressionSubmit = "{% url 'differential_expression_submit' %}"
-            const downloadFileURL = "{% url 'download_user_file' %}"
-            const urlGetUsersCandidatesLimited = "{% url 'user_candidates_limited_institution' %}"
-            const urlGetInstitutionsNonInExperiment = "{% url 'institution-non-experiments-list' %}"
-            const urlGetUsersNonInExperiment = "{% url 'user-non-experiments-list' %}"
-            const urlShareExperimentToInstitution = "{% url 'share-experiment-to-institution' %}"
-            const urlShareExperimentToUser = "{% url 'share-experiment-to-user' %}"
-            const urlGetSharedInstitution = "{% url 'shared-institution' %}"
-            const urlGetSharedUsers = "{% url 'shared-users' %}"
-            const urlPostSwitchInstitutionPublicView = "{% url 'switch-experiment-public-view' %}"
-            const urlPostRemoveInstitution = "{% url 'remove-institution' %}"
-            const urlPostRemoveUser = "{% url 'remove-user' %}"
-            const urlGetCommonSamples = "{% url 'get_number_samples_in_common' %}"
-            const urlGetCommonSamplesClinical = "{% url 'get_number_samples_in_common_clinical_validation' %}"
-            const urlGetCommonSamplesClinicalSource = "{% url 'get_number_samples_in_common_clinical_validation_source' %}"
-            const urlGetCommonSamplesOneFront = "{% url 'get_number_samples_in_common_one_front' %}"
-            const urlUnlinkClinicalSourceUserFile = "{% url 'unlink_clinical_source_user_file' %}"
-            const maximumNumberOfOpenTabs = Number.parseInt("{{ maximum_number_of_open_tabs }}")
-            const thresholdToConsiderOrdinal = Number.parseInt("{{ threshold_to_consider_ordinal }}")
         </script>
         {% render_bundle 'differentialExpression' 'js' %}
 {% endblock %}
\ No newline at end of file

From cb5b30d6d641319052233be7d1b272408cd27d8e Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Fri, 15 Aug 2025 21:19:09 -0300
Subject: [PATCH 08/47] Add R 4.4.2 and limma to Dockerfiles, update docs

Dockerfile and Dockerfile-celery now install R 4.4.2 and Bioconductor limma for differential expression analysis. Updated README to list R as a requirement and document the new Celery worker queue. docker-compose_dist.yml adds a differential-expression-worker service and includes it in the backend dependencies.
---
 Dockerfile              | 64 +++++++++++++++++++++++++----------------
 Dockerfile-celery       | 63 +++++++++++++++++++++++++---------------
 README.md               |  2 ++
 docker-compose_dist.yml | 16 +++++++++++
 4 files changed, 98 insertions(+), 47 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 6b106de2..4cc64ce5 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,47 +1,64 @@
 FROM python:3.12-slim-bookworm
 
 # Docker Files Vars
-ARG LISTEN_PORT 8000
-ARG LISTEN_IP "0.0.0.0"
+ARG LISTEN_PORT=8000
+ARG LISTEN_IP="0.0.0.0"
 
 # Default values for deploying with multiomix image
-ENV LISTEN_PORT $LISTEN_PORT
-ENV LISTEN_IP $LISTEN_IP
-ENV DJANGO_SETTINGS_MODULE "multiomics_intermediate.settings_prod"
-ENV RESULT_DATAFRAME_LIMIT_ROWS 500
-ENV TABLE_PAGE_SIZE 10
+ENV LISTEN_PORT=$LISTEN_PORT
+ENV LISTEN_IP=$LISTEN_IP
+ENV DJANGO_SETTINGS_MODULE="multiomics_intermediate.settings_prod"
+ENV RESULT_DATAFRAME_LIMIT_ROWS=500
+ENV TABLE_PAGE_SIZE=10
 
 # Modulector connection parameters
-ENV MODULECTOR_HOST "127.0.0.1"
-ENV MODULECTOR_PORT "8001"
+ENV MODULECTOR_HOST="127.0.0.1"
+ENV MODULECTOR_PORT="8001"
 
 # BioAPI connection parameters
-ENV BIOAPI_HOST "127.0.0.1"
-ENV BIOAPI_PORT "8002"
+ENV BIOAPI_HOST="127.0.0.1"
+ENV BIOAPI_PORT="8002"
 
 # PostgreSQL DB connection parameters
-ENV POSTGRES_USERNAME "multiomics"
-ENV POSTGRES_PASSWORD "multiomics"
-ENV POSTGRES_HOST "db"
-ENV POSTGRES_PORT 5432
-ENV POSTGRES_DB "multiomics"
+ENV POSTGRES_USERNAME="multiomics"
+ENV POSTGRES_PASSWORD="multiomics"
+ENV POSTGRES_HOST="db"
+ENV POSTGRES_PORT=5432
+ENV POSTGRES_DB="multiomics"
     
 # Mongo DB connection parameters
-ENV MONGO_USERNAME "multiomics"
-ENV MONGO_PASSWORD "multiomics"
-ENV MONGO_HOST "mongo"
-ENV MONGO_PORT 27017
-ENV MONGO_DB "multiomics"
+ENV MONGO_USERNAME="multiomics"
+ENV MONGO_PASSWORD="multiomics"
+ENV MONGO_HOST="mongo"
+ENV MONGO_PORT=27017
+ENV MONGO_DB="multiomics"
 
 # Redis
-ENV REDIS_HOST "redis"
-ENV REDIS_PORT 6379
+ENV REDIS_HOST="redis"
+ENV REDIS_PORT=6379
 
 # Installs system dependencies and Node.js
 RUN apt-get update && apt-get install -y python3-pip curl libcurl4-openssl-dev libssl-dev libxml2-dev \
     && curl -fsSL https://deb.nodesource.com/setup_20.x | bash - && apt-get install -y nodejs && mkdir /config \
     && mkdir /src
 
+# Instalar R 4.4.2 desde CRAN (Debian bookworm) y dependencias del sistema
+RUN set -eux; \
+  echo "deb http://deb.debian.org/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list; \
+  printf 'APT::Default-Release "%s";\n' "bookworm" > /etc/apt/apt.conf.d/00default-release; \
+  echo 'APT::Install-Recommends "false";' > /etc/apt/apt.conf.d/90no-recommends; \
+  printf 'Package: *\nPin: release a=unstable\nPin-Priority: 50\n' > /etc/apt/preferences.d/99pin-unstable; \
+  apt-get update; \
+  apt-get install -y --no-install-recommends \
+    ca-certificates curl gnupg build-essential gfortran libblas-dev liblapack-dev git \
+    libssl-dev libcurl4-openssl-dev libxml2-dev; \
+  apt-get install -y \
+    r-base=4.2.2.20221110-2 r-base-dev=4.2.2.20221110-2 r-recommended=4.2.2.20221110-2; \
+  rm -rf /var/lib/apt/lists/*
+
+# Instalar Bioconductor limma (stats y base vienen con R)
+RUN R -q -e 'options(repos=c(CRAN="https://cloud.r-project.org")); install.packages("BiocManager"); BiocManager::install(version="3.16", ask=FALSE); BiocManager::install("limma", ask=FALSE, update=FALSE)'
+
 # Installs Python dependencies and compiles the frontend
 ADD config/requirements.txt /config/
 WORKDIR /src
@@ -58,4 +75,3 @@ HEALTHCHECK --interval=5m --timeout=30s CMD ["/bin/bash", "-c", "/src/tools/chec
 ENTRYPOINT ["/bin/bash", "-c", "/src/entrypoint.sh"]
 
 EXPOSE $LISTEN_PORT
-
diff --git a/Dockerfile-celery b/Dockerfile-celery
index ea55bcba..a1822742 100644
--- a/Dockerfile-celery
+++ b/Dockerfile-celery
@@ -1,47 +1,64 @@
 FROM python:3.12-slim-bookworm
 
 # Docker Files Vars
-ARG LISTEN_PORT 8000
-ARG LISTEN_IP "0.0.0.0"
+ARG LISTEN_PORT=8000
+ARG LISTEN_IP="0.0.0.0"
 
 # Default values for deploying with multiomix image
-ENV LISTEN_PORT $LISTEN_PORT
-ENV LISTEN_IP $LISTEN_IP
-ENV DJANGO_SETTINGS_MODULE "multiomics_intermediate.settings_prod"
-ENV RESULT_DATAFRAME_LIMIT_ROWS 500
-ENV TABLE_PAGE_SIZE 10
+ENV LISTEN_PORT=$LISTEN_PORT
+ENV LISTEN_IP=$LISTEN_IP
+ENV DJANGO_SETTINGS_MODULE="multiomics_intermediate.settings_prod"
+ENV RESULT_DATAFRAME_LIMIT_ROWS=500
+ENV TABLE_PAGE_SIZE=10
 
 # Modulector connection parameters
-ENV MODULECTOR_HOST "127.0.0.1"
-ENV MODULECTOR_PORT "8001"
+ENV MODULECTOR_HOST="127.0.0.1"
+ENV MODULECTOR_PORT="8001"
 
 # BioAPI connection parameters
-ENV BIOAPI_HOST "127.0.0.1"
-ENV BIOAPI_PORT "8002"
+ENV BIOAPI_HOST="127.0.0.1"
+ENV BIOAPI_PORT="8002"
 
 # PostgreSQL DB connection parameters
-ENV POSTGRES_USERNAME "multiomics"
-ENV POSTGRES_PASSWORD "multiomics"
-ENV POSTGRES_HOST "db"
-ENV POSTGRES_PORT 5432
-ENV POSTGRES_DB "multiomics"
+ENV POSTGRES_USERNAME="multiomics"
+ENV POSTGRES_PASSWORD="multiomics"
+ENV POSTGRES_HOST="db"
+ENV POSTGRES_PORT=5432
+ENV POSTGRES_DB="multiomics"
     
 # Mongo DB connection parameters
-ENV MONGO_USERNAME "multiomics"
-ENV MONGO_PASSWORD "multiomics"
-ENV MONGO_HOST "mongo"
-ENV MONGO_PORT 27017
-ENV MONGO_DB "multiomics"
+ENV MONGO_USERNAME="multiomics"
+ENV MONGO_PASSWORD="multiomics"
+ENV MONGO_HOST="mongo"
+ENV MONGO_PORT=27017
+ENV MONGO_DB="multiomics"
 
 # Redis
-ENV REDIS_HOST "redis"
-ENV REDIS_PORT 6379
+ENV REDIS_HOST="redis"
+ENV REDIS_PORT=6379
 
 # Installs system dependencies
 RUN apt-get update && apt-get install -y python3-pip curl libcurl4-openssl-dev libssl-dev libxml2-dev \
     && mkdir /config \
     && mkdir /src
 
+# Instalar R 4.4.2 desde CRAN (Debian bookworm) y dependencias del sistema
+RUN set -eux; \
+  echo "deb http://deb.debian.org/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list; \
+  printf 'APT::Default-Release "%s";\n' "bookworm" > /etc/apt/apt.conf.d/00default-release; \
+  echo 'APT::Install-Recommends "false";' > /etc/apt/apt.conf.d/90no-recommends; \
+  printf 'Package: *\nPin: release a=unstable\nPin-Priority: 50\n' > /etc/apt/preferences.d/99pin-unstable; \
+  apt-get update; \
+  apt-get install -y --no-install-recommends \
+    ca-certificates curl gnupg build-essential gfortran libblas-dev liblapack-dev git \
+    libssl-dev libcurl4-openssl-dev libxml2-dev; \
+  apt-get install -y \
+    r-base=4.2.2.20221110-2 r-base-dev=4.2.2.20221110-2 r-recommended=4.2.2.20221110-2; \
+  rm -rf /var/lib/apt/lists/*
+
+# Instalar Bioconductor limma (stats y base vienen con R)
+RUN R -q -e 'options(repos=c(CRAN="https://cloud.r-project.org")); install.packages("BiocManager"); BiocManager::install(version="3.16", ask=FALSE); BiocManager::install("limma", ask=FALSE, update=FALSE)'
+
 # Installs Python dependencies
 ADD config/requirements_celery.txt /config/requirements.txt
 RUN pip install --upgrade pip && pip3 install -r /config/requirements.txt
diff --git a/README.md b/README.md
index 874a5f58..ab7094cd 100644
--- a/README.md
+++ b/README.md
@@ -15,6 +15,7 @@ This document is focused on the **development** of the system. If you are lookin
 - Node JS >= `20.x` (tested version: `20.x`)
 - [Modulector][modulector] `2.2.0`
 - [BioAPI][bioapi] `1.2.1`
+- R `4.4.2` (requerido para `differential-expression`)
 
 
 ## Installation 
@@ -66,6 +67,7 @@ Every time you want to work with Multiomix, you need to follow the below steps:
    1. `python3 -m celery -A multiomics_intermediate worker -l info -Q stats`
    1. `python3 -m celery -A multiomics_intermediate worker -l info -Q inference`
    1. `python3 -m celery -A multiomics_intermediate worker -l info -Q sync_datasets`
+   1. `python3 -m celery -A multiomics_intermediate worker -l info -Q differential_expression`
    1. If you want to check Task in the GUI you can run [Flower](https://flower.readthedocs.io/en/latest/index.html) `python3 -m celery -A multiomics_intermediate flower`
 
     **NOTE:** maybe in Windows is needed to add `--pool=solo` to the previous commands. Example: `python3 -m celery -A multiomics_intermediate worker -l info -Q correlation_analysis --concurrency 1 --pool=solo`
diff --git a/docker-compose_dist.yml b/docker-compose_dist.yml
index ca1ac3db..b8aa0abe 100644
--- a/docker-compose_dist.yml
+++ b/docker-compose_dist.yml
@@ -233,6 +233,21 @@ services:
             # REDIS_HOST: 'redis'
             # REDIS_PORT: 6379
 
+    # Celery worker for differential expression
+    differential-expression-worker:
+        image: omicsdatascience/multiomix:5.6.0-celery
+        restart: 'always'
+        depends_on:
+            - db
+            - mongo
+        volumes:
+            - media_data:/src/media
+        environment:
+            <<: *common-variables
+            QUEUE_NAME: 'differential_expression'  # This MUST NOT be changed
+            CONCURRENCY: 2
+            # PostgreSQL, Mongo y Redis usan los valores por defecto del resto de servicios
+
     # Django backend service
     multiomix:
         image: omicsdatascience/multiomix:5.6.0
@@ -290,6 +305,7 @@ services:
             - stats-worker
             - inference-worker
             - sync-datasets-worker
+            - differential-expression-worker
 
 volumes:
     mongo_data:

From 18860f9fdec31772a26eeb340a1d1404de1d53b7 Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Sun, 17 Aug 2025 19:06:43 -0300
Subject: [PATCH 09/47] Add endpoint to stop differential expression experiment

Introduces DifferentialExpressionStop API view and URL to allow authenticated users to stop a running differential expression experiment. Includes permission checks, state validation, and integration with abortable Celery tasks.
---
 src/differential_expression/urls.py  |  1 +
 src/differential_expression/views.py | 81 ++++++++++++++++++++++++----
 2 files changed, 72 insertions(+), 10 deletions(-)

diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index 5c2a34ac..05fe0eeb 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -7,4 +7,5 @@
     path('<int:pk>/results/', views.DifferentialExpressionResults.as_view()),
     path('<int:pk>/significant-genes/', views.DifferentialExpressionSignificantGenes.as_view()),
     path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
+    path('stop-experiment', views.DifferentialExpressionStop.as_view(), name='differential_expression_stop'),
 ]
\ No newline at end of file
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index c41b29a3..569e5a25 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -29,6 +29,9 @@
 
 from .tasks import eval_differential_expression_experiment
 
+from celery.contrib.abortable import AbortableAsyncResult
+from differential_expression.models import DifferentialExpressionExperimentState
+
 
 def create_differential_expression_source(
     source_type: int,
@@ -154,6 +157,8 @@ class DifferentialExpressionSubmit(APIView):
     Endpoint to submit a differential expression experiment.
     """
 
+    permission_classes = [permissions.IsAuthenticated]
+
     def post(self, request: Request):
         """
         Endpoint to submit a differential expression experiment.
@@ -161,7 +166,7 @@ def post(self, request: Request):
         with transaction.atomic():
             # Get basic experiment data
             post_data = getattr(request, 'data', {}) or getattr(request, 'POST', {})
-            
+
             name = post_data.get('name', 'Differential Expression Experiment')
             description = post_data.get('description', '')
 
@@ -242,7 +247,7 @@ def post(self, request: Request):
             # Start the async task
             async_res = eval_differential_expression_experiment.apply_async(
                 (experiment.pk,), queue='differential_expression')
-            
+
             experiment.task_id = async_res.task_id
             experiment.save(update_fields=['task_id'])
 
@@ -259,11 +264,11 @@ class DifferentialExpressionResults(generics.ListAPIView):
     filter_backends = [filters.OrderingFilter, DjangoFilterBackend]
     ordering_fields = ['adj_p_val', 'log_fc', 'p_value', 'ave_expr']
     ordering = ['adj_p_val']  # Default ordering by adjusted p-value
-    
+
     def get_queryset(self):
         experiment_id = self.kwargs.get('pk')
         experiment = get_object_or_404(DifferentialExpressionExperiment, pk=experiment_id)
-        
+
         # Check permissions
         user = self.request.user
         if not (experiment.is_public or
@@ -271,7 +276,7 @@ def get_queryset(self):
                 experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
                 experiment.shared_users.filter(id=user.id).exists()):
             raise ValidationError('You do not have permission to access this experiment.')
-        
+
         return experiment.results.all()
 
 
@@ -285,11 +290,11 @@ class DifferentialExpressionSignificantGenes(generics.ListAPIView):
     filter_backends = [filters.OrderingFilter]
     ordering_fields = ['adj_p_val', 'log_fc', 'p_value', 'ave_expr']
     ordering = ['adj_p_val']  # Default ordering by adjusted p-value
-    
+
     def get_queryset(self):
         experiment_id = self.kwargs.get('pk')
         experiment = get_object_or_404(DifferentialExpressionExperiment, pk=experiment_id)
-        
+
         # Check permissions (same logic as DifferentialExpressionDetail)
         user = self.request.user
         if not (experiment.is_public or
@@ -297,18 +302,74 @@ def get_queryset(self):
                 experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
                 experiment.shared_users.filter(id=user.id).exists()):
             raise ValidationError('You do not have permission to access this experiment.')
-        
+
         # Get query parameters for filtering
         try:
             p_threshold = float(self.request.query_params.get('p_threshold', 0.05))
             fc_threshold = float(self.request.query_params.get('fc_threshold', 2.0))
         except ValueError as exc:
             raise ValidationError('Invalid threshold values. Must be numeric.') from exc
-        
+
         # Validate thresholds
         if p_threshold < 0 or p_threshold > 1:
             raise ValidationError('p_threshold must be between 0 and 1')
         if fc_threshold < 0:
             raise ValidationError('fc_threshold must be positive')
-        
+
         return experiment.get_significant_genes(p_threshold, fc_threshold)
+
+
+class DifferentialExpressionStop(APIView):
+    """
+    Endpoint to stop a differential expression experiment.
+    """
+    permission_classes = [permissions.IsAuthenticated]
+
+    def get(self, request: Request):
+        experiment_id = request.GET.get('experimentId')
+        if not experiment_id:
+            raise ValidationError('experimentId is required.')
+
+        try:
+            experiment_id = int(experiment_id)
+        except (ValueError, TypeError) as exc:
+            raise ValidationError('Invalid experimentId') from exc
+
+        experiment = get_object_or_404(DifferentialExpressionExperiment, pk=experiment_id)
+
+        user = request.user
+        if not (experiment.is_public or
+                experiment.user == user or
+                experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
+                experiment.shared_users.filter(id=user.id).exists()):
+            raise ValidationError('You do not have permission to access this experiment.')
+
+        # Validaciones de estado y task
+        if not experiment.task_id:
+            return Response({'ok': False, 'detail': 'The experiment does not have an associated task.'})
+
+        # Si ya no está en curso, no hay nada que detener
+        if experiment.state in [
+            DifferentialExpressionExperimentState.COMPLETED,
+            DifferentialExpressionExperimentState.STOPPED,
+            DifferentialExpressionExperimentState.FINISHED_WITH_ERROR,
+            DifferentialExpressionExperimentState.TIMEOUT_EXCEEDED,
+            DifferentialExpressionExperimentState.REACHED_ATTEMPTS_LIMIT,
+            DifferentialExpressionExperimentState.EMPTY_DATASET,
+            DifferentialExpressionExperimentState.NO_SAMPLES_IN_COMMON,
+            DifferentialExpressionExperimentState.NO_FEATURES_FOUND,
+        ]:
+            return Response({'ok': False, 'detail': f'The experiment is not running. Status: {experiment.state}'})
+
+        # Intentar abortar la tarea AbortableTask
+        try:
+            async_res = AbortableAsyncResult(experiment.task_id)
+            aborted = async_res.abort()  # Señala a la tarea que debe abortar (self.is_aborted() == True)
+        except Exception as e:
+            return Response({'ok': False, 'detail': f'The task could not be stopped: {e}'})
+
+        # Marcar el experimento como STOPPING; la tarea lo marcará como STOPPED en el finally
+        experiment.state = DifferentialExpressionExperimentState.STOPPING
+        experiment.save(update_fields=['state'])
+
+        return Response({'ok': bool(aborted)})

From da50ff64b4a43f28cb93b1f954186b664acae9e9 Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Tue, 2 Sep 2025 20:13:48 -0300
Subject: [PATCH 10/47] form

---
 src/api_service/utils.py                      |   2 +
 src/differential_expression/urls.py           |   4 +-
 src/differential_expression/views.py          | 178 ++++-
 .../frontend/src/components/MainNavbar.tsx    |   2 +-
 .../DifferentialExpressionForm.tsx            | 664 +++++++++++++++---
 ...entialExpressionInputClinicalAttribute.tsx |  31 +
 .../DifferentialExpressionPanel.tsx           |  68 +-
 .../src/css/differential-expression.css       |   8 +
 .../frontend/src/utils/django_interfaces.ts   |  21 +-
 .../frontend/differential-expression.html     |   3 +
 10 files changed, 868 insertions(+), 113 deletions(-)
 create mode 100644 src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx

diff --git a/src/api_service/utils.py b/src/api_service/utils.py
index 511cc9fa..ff242e33 100644
--- a/src/api_service/utils.py
+++ b/src/api_service/utils.py
@@ -131,5 +131,7 @@ def get_cgds_dataset(cgds_study: CGDSStudy, file_type: FileType) -> Optional[CGD
         return cgds_study.cna_dataset
     elif file_type == FileType.METHYLATION:
         return cgds_study.methylation_dataset
+    elif file_type == FileType.CLINICAL:
+        return cgds_study.clinical_patient_dataset
     else:
         return None
diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index 05fe0eeb..5b1f2b78 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -8,4 +8,6 @@
     path('<int:pk>/significant-genes/', views.DifferentialExpressionSignificantGenes.as_view()),
     path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
     path('stop-experiment', views.DifferentialExpressionStop.as_view(), name='differential_expression_stop'),
-]
\ No newline at end of file
+    path('get-common-samples-differential-experiment', views.GetCommonSamplesDifferentialExperiment.as_view(), name='get_common_samples_differential_experiment'),
+    path('get-common-samples-one-front-differential-experiment', views.GetCommonSamplesDifferentialOneFrontExperiment.as_view(), name='get_common_samples_one_front_differential_experiment'),
+    ]
\ No newline at end of file
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 569e5a25..c8335e19 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -1,3 +1,5 @@
+import json
+
 from django.db import transaction
 from django.db.models import Q
 
@@ -9,7 +11,7 @@
 from rest_framework.response import Response
 from rest_framework.views import APIView
 
-from api_service.enums import SourceType
+from api_service.enums import SourceType, CommonSamplesStatusErrorCode
 from api_service.utils import get_cgds_dataset
 from common.pagination import StandardResultsSetPagination
 from datasets_synchronization.models import CGDSStudy
@@ -31,6 +33,11 @@
 
 from celery.contrib.abortable import AbortableAsyncResult
 from differential_expression.models import DifferentialExpressionExperimentState
+from common.functions import get_enum_from_value, get_intersection, encode_json_response_status
+from common.response import ResponseStatus
+from common.enums import ResponseCode
+from typing import Optional, Dict, Tuple, List, Type, OrderedDict, Union, cast, Any
+from datasets_synchronization.models import CGDSDataset
 
 
 def create_differential_expression_source(
@@ -172,12 +179,15 @@ def post(self, request: Request):
 
             # Clinical source
             clinical_source_type = post_data.get('clinicalType')
+            print(clinical_source_type)
+
             if clinical_source_type:
                 clinical_source_type = int(clinical_source_type)
                 clinical_source, clinical_aux = create_differential_expression_source(
                     clinical_source_type, request, FileType.CLINICAL, 'clinical')
                 # Select the valid one (if it's a CGDSStudy it needs clinical_aux as it has both needed CGDSDatasets)
                 clinical_source = clinical_aux if clinical_aux is not None else clinical_source
+                print(clinical_source, clinical_aux)
             else:
                 clinical_source = None
 
@@ -373,3 +383,169 @@ def get(self, request: Request):
         experiment.save(update_fields=['state'])
 
         return Response({'ok': bool(aborted)})
+class GetCommonSamplesDifferentialExperiment(APIView):
+    """Gets the number of in common samples between two datasets"""
+
+    permission_classes = [permissions.IsAuthenticated]
+
+    def get(self, request: Request):
+        mrna_source_id = request.GET.get('mRNASourceId')
+        mrna_source_type = request.GET.get('mRNASourceType')
+        clinical_source_id = request.GET.get('clinicalSourceId')
+        clinical_source_type = request.GET.get('clinicalSourceType')
+        if None in [mrna_source_id, mrna_source_type, clinical_source_id,
+                    clinical_source_type]:
+            response = {
+                'status': ResponseStatus(
+                    ResponseCode.ERROR,
+                    message='Invalid request params',
+                    internal_code=CommonSamplesStatusErrorCode.INVALID_PARAMS
+                ),
+            }
+        else:
+            # Cast parameters
+            mrna_source_id = int(mrna_source_id)
+            mrna_source_type = get_enum_from_value(
+                int(mrna_source_type), SourceType)
+
+            clinical_source_id = int(clinical_source_id)
+            clinical_source_type = get_enum_from_value(int(clinical_source_type), SourceType)
+
+            # Gets df
+            samples_list_mrna, response = get_samples_list(
+                mrna_source_id,
+                mrna_source_type,
+                FileType.MRNA,
+                request.user
+            )
+
+            # Response will be != None if an error occurred
+            if response is None:
+                samples_list_clinical, response = get_samples_list(
+                    clinical_source_id,
+                    clinical_source_type,
+                    FileType.CLINICAL,
+                    request.user
+                )
+                intersection = get_intersection(samples_list_mrna, samples_list_clinical)
+                # Gets intersection
+
+                if response is None:
+                    response = {
+                        'status': ResponseStatus(ResponseCode.SUCCESS),
+                        'data': {
+                            'number_samples_mrna': len(samples_list_mrna) if samples_list_mrna is not None else 0,
+                            'number_samples_clinical': len(
+                                samples_list_clinical) if samples_list_clinical is not None else 0,
+                            'number_samples_in_common': intersection.size
+                        }
+                    }
+
+        # Formats to JSON the ResponseStatus object
+        return encode_json_response_status(response)
+
+class GetCommonSamplesDifferentialOneFrontExperiment(APIView):
+    permission_classes = [permissions.IsAuthenticated]
+    """Gets the number of in common samples between two datasets, one in the backend and other in the frontend"""
+
+    def post(self, request: Request):
+        post_data = getattr(request, 'data', {}) or getattr(request, 'POST', {})
+        headers_in_front: Optional[List[str]] = post_data.get('headersColumnsNames')
+        other_source_id = post_data.get('otherSourceId')
+        other_source_type = post_data.get('otherSourceType')
+        other_source_file_type = post_data.get('otherSourceFileType')
+
+        if headers_in_front is None or other_source_id is None or other_source_type is None or other_source_file_type is None:
+            response = {
+                'status': ResponseStatus(
+                    ResponseCode.ERROR,
+                    message='Invalid request params',
+                    internal_code=CommonSamplesStatusErrorCode.INVALID_PARAMS
+                ),
+            }
+        else:
+            # Cast parameters
+            other_source_id = int(other_source_id)
+            other_source_type = get_enum_from_value(
+                int(other_source_type), SourceType)
+
+            # Gets df
+            samples_list_1, response = get_samples_list(
+                other_source_id,
+                other_source_type,
+                other_source_file_type,
+                request.user
+            )
+
+            # Response will be != None if an error occurred
+            if response is None:
+                intersection: np.ndarray = get_intersection(
+                    samples_list_1, headers_in_front)
+                response = {
+                    'status': ResponseStatus(ResponseCode.SUCCESS),
+                    'data': {
+                        'number_samples_backend': len(samples_list_1) if samples_list_1 else 0,
+                        'number_samples_in_common': intersection.size
+                    }
+                }
+
+        # Formats to JSON the ResponseStatus object
+        return encode_json_response_status(response)
+
+def get_samples_list(
+        id_source: int,
+        type_source: Optional[SourceType],
+        file_type: Optional[FileType],
+        user
+) -> Tuple[Optional[List[str]], Optional[Dict]]:
+    """
+    Gets a DataFrame from the file retrieve from DB or MongoDB with an id and SourceType.
+    @param id_source: ID of the UserFile/CGDSDataset to retrieve.
+    @param type_source: Source type to check if it's a UserFile or a CGDSDataset.
+    @param file_type: FileType (mRNA, miRNA, etc.) to get the corresponding CGDSDataset.
+    @param user: Current logged user to retrieve only his datasets.
+    @return: A DataFrame (if corresponds) and a Response dict (the dataset doesn't exist).
+    """
+    list_of_samples = None
+    response = None
+    if type_source is None:
+        response = {
+            'status': ResponseStatus(
+                ResponseCode.ERROR,
+                message=f'The source type {type_source} does not exist',
+                internal_code=CommonSamplesStatusErrorCode.SOURCE_TYPE_DOES_NOT_EXISTS
+            ),
+        }
+    elif type_source == SourceType.UPLOADED_DATASETS:
+        try:
+            user_file = get_an_user_file(user=user, user_file_pk=id_source)
+            print(user_file)
+            if file_type == FileType.CLINICAL:
+                list_of_samples = user_file.get_first_column_of_all_rows()
+            else:
+                list_of_samples = user_file.get_column_names()
+        except UserFile.DoesNotExist:
+            response = {
+                'status': ResponseStatus(
+                    ResponseCode.ERROR,
+                    message=f'The UserFile with id = {id_source} does not exist',
+                    internal_code=CommonSamplesStatusErrorCode.DATASET_DOES_NOT_EXISTS
+                ),
+            }
+    elif type_source == SourceType.CGDS:
+        try:
+            # Gets the CGDS Study
+            cgds_study = CGDSStudy.objects.get(pk=id_source)
+
+            # Gets the corresponding Study's Dataset
+            cgds_dataset = get_cgds_dataset(cgds_study, file_type)
+        except CGDSDataset.DoesNotExist:
+            response = {
+                'status': ResponseStatus(
+                    ResponseCode.ERROR,
+                    message=f'The CGDS dataset with id = {id_source} does not exist',
+                    internal_code=CommonSamplesStatusErrorCode.DATASET_DOES_NOT_EXISTS
+                ),
+            }
+
+    return list_of_samples, response
diff --git a/src/frontend/static/frontend/src/components/MainNavbar.tsx b/src/frontend/static/frontend/src/components/MainNavbar.tsx
index cf782d2f..508735f1 100644
--- a/src/frontend/static/frontend/src/components/MainNavbar.tsx
+++ b/src/frontend/static/frontend/src/components/MainNavbar.tsx
@@ -235,7 +235,7 @@ const MainNavbar = (props: MainNavbarProps) => {
                                 {/* Differential Expression panel */}
                                 <Dropdown.Item
                                     text='Differential expression'
-                                    icon='list layout'
+                                    icon='buromobelexperte'
                                     as='a' href={urlDifferentialExpression}
                                     active={props.activeItem === 'differential-expression'}
                                 />
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
index 7288c424..df91a300 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
@@ -1,14 +1,23 @@
-import React, { useState } from 'react'
-import { Form, Header, Icon, Input, Label, Segment, TextArea } from 'semantic-ui-react'
+import React, { useRef, useState } from 'react'
+import { Button, Form, Header, Icon, Label, PopupContentProps, Segment, SemanticShorthandItem } from 'semantic-ui-react'
 import { SourceForm } from '../pipeline/SourceForm'
 import { SingleRangeSlider } from 'neo-react-semantic-ui-range'
-import { FileType, Source, SourceType } from '../../utils/interfaces'
-import { cleanRef, getDefaultSource, getFilenameFromSource } from '../../utils/util_functions'
-import { DjangoCGDSStudy, DjangoUserFile } from '../../utils/django_interfaces'
+import { FileType, KySearchParams, Nullable, Source, SourceType } from '../../utils/interfaces'
+import { cleanRef, getDefaultSource, getDjangoHeader, getFilenameFromSource, getFileSizeInMB, getInputFileCSVColumns } from '../../utils/util_functions'
+import { DjangoCGDSStudy, DjangoNumberSamplesInCommonMrnaClinicalResult, DjangoNumberSamplesInCommonOneFrontResult, DjangoResponseCode, DjangoUserFile } from '../../utils/django_interfaces'
+import { InfoPopup } from '../pipeline/experiment-result/gene-gem-details/InfoPopup'
+import ky from 'ky'
+import { MAX_FILE_SIZE_IN_MB_WARN } from '../../utils/constants'
+import { intersection } from 'lodash'
+import { DifferentialExpressionInputClinicalAttribute } from './DifferentialExpressionInputClinicalAttribute'
 
-interface IDifferentialExpressionForm extends IDifferentialExpressionFormData {
-    isEditing: boolean
-}
+// Define the possible field names for number of samples
+type NumberOfSamplesFields = 'numberOfSamplesMRNA' | 'numberOfSamplesClinical'
+
+declare const urlDifferentialExpressionSubmit: string
+declare const urlGetCommonSamplesDiferentialExperiment: string
+declare const urlGetCommonSamplesOneFrontDiferentialExperiment: string
+declare const urlGetClinicalAttributes: string
 
 /** Available types of Sources for a DifferentialExpressionForm. */
 type SourceStateDifferentialExpression = 'clinicalSource' | 'mRNASource'
@@ -23,9 +32,23 @@ interface IDifferentialExpressionFormData {
     differentialExpressionDescription: string,
     /** Differential Expression description. */
     differentialExpressionName: string,
-    /** Percentile threshold. */
-    percentileThreshold: number,
+    /** Umbral de Percentil para el filtrado de genes de baja expresión. */
+    thresholdPercentile: number,
+    /** Umbral de varianza para el filtrado de genes. */
+    thresholdStd: number
+    /** top */
+    top: number,
 
+    numberOfSamplesMRNA: number,
+    numberOfSamplesClinical: number,
+    numberOfSamplesInCommon: number,
+    gettingCommonSamples: boolean,
+    clinicalAttribute: string,
+}
+interface IDifferentialExpressionForm extends IDifferentialExpressionFormData {
+    isEditing: boolean,
+    isLoading: boolean,
+    optionsClinicalAttributes: string[],
 }
 const cleanForm: IDifferentialExpressionForm = {
     mRNASource: getDefaultSource(),
@@ -33,11 +56,21 @@ const cleanForm: IDifferentialExpressionForm = {
     isEditing: false,
     differentialExpressionDescription: '',
     differentialExpressionName: '',
-    percentileThreshold: 0.15,
+    clinicalAttribute: '',
+    thresholdPercentile: 0.15,
+    thresholdStd: 0.0001,
+    top: 100,
+    isLoading: false,
+    numberOfSamplesMRNA: 0,
+    numberOfSamplesClinical: 0,
+    numberOfSamplesInCommon: 0,
+    gettingCommonSamples: false,
+    optionsClinicalAttributes: [],
 }
 
 export const DifferentialExpressionForm = () => {
-    const [form, setForm] = useState<IDifferentialExpressionForm>(cleanForm);
+    const [form, setForm] = useState<IDifferentialExpressionForm>(cleanForm)
+    const abortController = useRef(new AbortController())
 
     /**
      * Change the source state to submit a pipeline
@@ -54,15 +87,11 @@ export const DifferentialExpressionForm = () => {
         source.selectedExistingFile = null
         source.CGDSStudy = null
         cleanRef(source.newUploadedFileRef)
-        console.log(source)
-        console.log('---')
         // After update state
         setForm(prevState => ({
             ...prevState,
             [sourceStateName]: source,
         }))
-        console.log(form)
-        console.log('---')
 
         updateSourceFilenamesAndCommonSamples()
     }
@@ -103,6 +132,30 @@ export const DifferentialExpressionForm = () => {
         updateSourceFilenamesAndCommonSamples()
     }
 
+    /**
+     * function to handle the update de select clinical attribute.
+     */
+    const updateSelectClinicalAttribute = () => {
+        if (form.clinicalSource.newUploadedFileRef.current && form.clinicalSource.selectedExistingFile === null) {
+            getInputFileCSVColumns(form.clinicalSource.newUploadedFileRef.current.files[0]).then((clinicalHeadersColumnsNames) => {
+                setForm(prevState => ({ ...prevState, optionsClinicalAttributes: clinicalHeadersColumnsNames }))
+            })
+        } else if (form.clinicalSource.selectedExistingFile?.id || form.clinicalSource.CGDSStudy?.id) {
+            const idToSearch = form.clinicalSource.selectedExistingFile?.id ?? form.clinicalSource.CGDSStudy?.id
+            const myHeaders = getDjangoHeader()
+            ky.get(urlGetClinicalAttributes + `${idToSearch}/`, { timeout: 60000, headers: myHeaders, signal: abortController.current.signal }).then((response) => {
+                response.json().then((clinicalAttributes: string[]) => {
+                    setForm(prevState => ({ ...prevState, optionsClinicalAttributes: clinicalAttributes }))
+                }).catch((err) => {
+                    console.error('Error parsing JSON ->', err)
+                })
+            }).catch((err) => {
+                if (!abortController.current.signal.aborted) {
+                    console.error('Error getting clinical attributes', err)
+                }
+            })
+        }
+    }
 
     /**
      * Handles file input changes to set data to show in form
@@ -122,6 +175,7 @@ export const DifferentialExpressionForm = () => {
             },
 
         }))
+        updateSelectClinicalAttribute()
     }
 
     /**
@@ -130,122 +184,518 @@ export const DifferentialExpressionForm = () => {
      */
     const updateSourceFilenamesAndCommonSamples = () => {
         updateSourceFilenames()
+        checkCommonSamples()
     }
 
-
     /**
- * Callback when a new file is selected in the uncontrolled component
- * (input type=file)
- */
-    const selectNewFile = () => { updateSourceFilenamesAndCommonSamples() }
+     * Callback when a new file is selected in the uncontrolled component
+     * (input type=file)
+     */
+    const selectNewFile = (e:any) => { 
+        console.log(e)
+        updateSourceFilenamesAndCommonSamples() }
 
     /**
      * change name or description of manual form
      * @param value new value for input form
      * @param name type of input to change
      */
-    const handleChangeForm = (value: string | number, name: 'differentialExpressionName' | 'differentialExpressionDescription' | 'coefficientThreshold') => {
+    const handleChangeForm = (value: string | number, name: keyof IDifferentialExpressionFormData) => {
         setForm(prevState => ({
             ...prevState,
             [name]: value,
         }))
     }
 
+    /**
+     * Function to convert a number to scientific notation
+     * @param value Number to convert
+     * @param sigfigs Significant figures to use in the conversion
+     * @returns String in scientific notation
+     */
+    function toScientific (value: string, sigfigs?: number): string {
+        const num = Number(String(value).trim().replace(',', '.'))
+
+        if (!Number.isFinite(num)) {
+            throw new Error('Número inválido')
+        }
+
+        // toExponential(n) usa n dígitos después del punto ⇒ sigfigs - 1
+        return sigfigs && sigfigs > 0
+            ? num.toExponential(sigfigs - 1)
+            : num.toExponential()
+    }
+
+    const handleSubmit = () => {
+        const myHeaders = getDjangoHeader()
+        const body = {
+            name: form.differentialExpressionName,
+            description: form.differentialExpressionDescription,
+            clinicalType: form.clinicalSource.type,
+            mRNAType: form.mRNASource.type,
+            clinicalAttribute: form.clinicalAttribute,
+            thresholdPercentile: form.thresholdPercentile,
+            threshold: form.thresholdStd,
+            top: form.top,
+        }
+        ky.post(urlDifferentialExpressionSubmit, { headers: myHeaders, json: body }).then((response) => {
+            response.json().then(() => {
+                console.log(response)
+            }).catch((err) => {
+                console.error('Error parsing JSON ->', err)
+            })
+        }).catch((err) => {
+            console.error('Error getting users ->', err)
+        })
+    }
+
+    /**
+     * Gets the id of the source hosted in backend to send to the service
+     * of number of samples in common
+     * @param source Source to get its id
+     * @returns Id of the source or null if it's not been selected yet
+     */
+    const getIdInBackend = (source: Source): Nullable<number> => {
+        if (source.type === SourceType.UPLOADED_DATASETS && source.selectedExistingFile !== null) {
+            return source.selectedExistingFile.id ?? null
+        }
+
+        if (source.type === SourceType.CGDS && source.CGDSStudy !== null) {
+            return source.CGDSStudy.id ?? null
+        }
+
+        return null
+    }
+
+    /**
+     * General method to avoid duplicated code when the reading
+     * of a loaded user's file fails
+     * @param event Event of error
+     */
+    const errorReadingFileInInput = (event) => {
+        resetAllNumberOfSamples()
+        console.log('Error reading user\'s file')
+        console.log(event.target.error.name)
+    }
+
+    /**
+     * Gets the number of samples in common between both selected datasets
+     * one in frontend, other in backend
+     * @param mRNASourceIsInBackend Flag to know which dataset is in frontend and backend
+     */
+    const checkCommonSamplesOneFrontOneBack = (mRNASourceIsInBackend: boolean) => {
+        let sourceInFront: Source
+        let sourceFrontNumberOfSampleName: NumberOfSamplesFields, sourceBackNumberOfSampleName: NumberOfSamplesFields
+        let otherSourceId: number, otherSourceType: Nullable<SourceType>
+        let otherSourceFileType: FileType
+        const mRNASource = form.mRNASource
+        const clinicalSource = form.clinicalSource
+
+        if (mRNASourceIsInBackend) {
+            // If mRNA is in backend, GEM is in frontend
+            const idInBackend = getIdInBackend(mRNASource)
+
+            if (idInBackend === null) {
+                return
+            }
+
+            sourceInFront = clinicalSource
+            sourceFrontNumberOfSampleName = 'numberOfSamplesClinical'
+            sourceBackNumberOfSampleName = 'numberOfSamplesMRNA'
+            otherSourceId = idInBackend
+            otherSourceType = mRNASource.type
+            otherSourceFileType = FileType.CLINICAL
+        } else {
+            const idInBackend = getIdInBackend(clinicalSource)
+
+            if (idInBackend === null) {
+                return
+            }
+
+            sourceInFront = mRNASource
+            sourceFrontNumberOfSampleName = 'numberOfSamplesMRNA'
+            sourceBackNumberOfSampleName = 'numberOfSamplesClinical'
+            otherSourceId = idInBackend
+            otherSourceType = clinicalSource.type
+            otherSourceFileType = FileType.MRNA
+        }
+
+        // We need both datasets!
+        const sourceCurrentRef = sourceInFront.newUploadedFileRef.current
+
+        if (!sourceCurrentRef || sourceCurrentRef.files.length === 0) {
+            resetAllNumberOfSamples()
+            return
+        }
+
+        const fileSizeInMB = getFileSizeInMB(sourceInFront.newUploadedFileRef.current.files[0].size)
+
+        if (fileSizeInMB < MAX_FILE_SIZE_IN_MB_WARN) {
+            const file = sourceInFront.newUploadedFileRef.current.files[0]
+            getInputFileCSVColumns(file).then((headersColumnsNames) => {
+                // Sets the Request's Headers
+                const myHeaders = getDjangoHeader()
+
+                // Sends an array of headers to compare in server
+                const jsonData = {
+                    headersColumnsNames,
+                    otherSourceId,
+                    otherSourceType,
+                    otherSourceFileType
+                }
+                setForm(prevState => ({ ...prevState, gettingCommonSamples: true }))
+                ky.post(urlGetCommonSamplesOneFrontDiferentialExperiment, { json: jsonData, headers: myHeaders }).then((response) => {
+                    response.json().then((jsonResponse: DjangoNumberSamplesInCommonOneFrontResult) => {
+                        if (jsonResponse.status.code === DjangoResponseCode.SUCCESS) {
+                            // For front Source subtracts 1 to not have in count the first column of the file
+                            setForm(prevState => ({
+                                ...prevState,
+                                gettingCommonSamples: false,
+                                [sourceFrontNumberOfSampleName]: Math.max(headersColumnsNames.length - 1, 0),
+                                [sourceBackNumberOfSampleName]: jsonResponse.data.number_samples_backend,
+                                numberOfSamplesInCommon: jsonResponse.data.number_samples_in_common
+                            }))
+                        }
+                    }).catch((err) => {
+                        console.error('Error parsing JSON ->', err)
+                    })
+                }).catch((err) => {
+                    setForm(prevState => ({ ...prevState, gettingCommonSamples: false }))
+                    console.error('Error getting user experiments', err)
+                })
+            }).catch(errorReadingFileInInput)
+        }
+    }
+
+    /**
+     * Gets the number of samples in common between both selected datasets
+     * hosted in backend
+     */
+    const checkCommonSamplesInBackend = () => {
+        const mRNASourceId = getIdInBackend(form.mRNASource)
+        const clinicalSourceId = getIdInBackend(form.clinicalSource)
+
+        if (mRNASourceId !== null && clinicalSourceId !== null) {
+            const searchParams = {
+                mRNASourceId,
+                mRNASourceType: form.mRNASource.type,
+                clinicalSourceId,
+                clinicalSourceType: form.clinicalSource.type,
+            }
+            setForm(prevState => ({ ...prevState, gettingCommonSamples: true }))
+
+            ky.get(urlGetCommonSamplesDiferentialExperiment, { signal: abortController.current.signal, searchParams: searchParams as KySearchParams }).then((response) => {
+                setForm(prevState => ({
+                    ...prevState,
+                    gettingCommonSamples: false
+                }))
+                response.json().then((jsonResponse: DjangoNumberSamplesInCommonMrnaClinicalResult) => {
+                    if (jsonResponse.status.code === DjangoResponseCode.SUCCESS) {
+                        setForm(prevState => ({
+                            ...prevState,
+                            numberOfSamplesMRNA: jsonResponse.data.number_samples_mrna,
+                            numberOfSamplesClinical: jsonResponse.data.number_samples_clinical,
+                            numberOfSamplesInCommon: jsonResponse.data.number_samples_in_common
+                        }))
+                    }
+                }).catch((err) => {
+                    console.error('Error parsing JSON ->', err)
+                })
+            }).catch((err) => {
+                if (!abortController.current.signal.aborted) {
+                    setForm(prevState => ({
+                        ...prevState,
+                        gettingCommonSamples: false
+                    }))
+                }
+
+                console.error('Error getting user experiments', err)
+            })
+        }
+    }
+
+    /**
+     * Check if a Source is hosted in the backend
+     * @param source Source to check
+     * @returns True if the Source is hosted in the backend. False otherwise
+     */
+    const isDatasetInBackend = (source: Source): boolean => {
+        return source.type === SourceType.UPLOADED_DATASETS || source.type === SourceType.CGDS
+    }
+
+    /**
+     * Resets all the number of samples
+     */
+    const resetAllNumberOfSamples = () => {
+        setForm(prevState => ({
+            ...prevState,
+            numberOfSamplesMRNA: 0,
+            numberOfSamplesClinical: 0,
+            numberOfSamplesInCommon: 0
+        })
+        )
+    }
+
+    /**
+     * Checks if there are common samples between two selected sources
+     * to show in the new experiment form
+     */
+    const checkCommonSamples = () => {
+        // It needs both sources!
+        if (form.mRNASource.type === SourceType.NONE || form.clinicalSource.type === SourceType.NONE) {
+            resetAllNumberOfSamples()
+            return
+        }
+
+        const mRNASourceIsInBackend = isDatasetInBackend(form.mRNASource)
+        const clinicalSourceIsInBackend = isDatasetInBackend(form.clinicalSource)
+        // If both datasets are hosted in backend, checks in server
+
+        if (mRNASourceIsInBackend && clinicalSourceIsInBackend) {
+            checkCommonSamplesInBackend()
+        } else if (mRNASourceIsInBackend || clinicalSourceIsInBackend) {
+            checkCommonSamplesOneFrontOneBack(mRNASourceIsInBackend)
+        } else {
+            checkCommonSamplesInFrontend()
+        }
+    }
+
+    /**
+     * Gets the number of samples in common between both selected datasets
+     * loaded in HTML file inputs
+     */
+    const checkCommonSamplesInFrontend = () => {
+        const mRNASource = form.mRNASource
+        const clinicalSource = form.clinicalSource
+
+        // We need both datasets!
+        if (mRNASource.newUploadedFileRef.current.files.length === 0 ||
+            clinicalSource.newUploadedFileRef.current.files.length === 0) {
+            resetAllNumberOfSamples()
+            return
+        }
+
+        // Reads first file
+        const mRNAFile = mRNASource.newUploadedFileRef.current.files[0]
+        getInputFileCSVColumns(mRNAFile).then((mRNAHeadersColumnsNames) => {
+            // Reads second file
+            const clinicalFile = clinicalSource.newUploadedFileRef.current.files[0]
+            getInputFileCSVColumns(clinicalFile).then((clinicalHeadersColumnsNames) => {
+                // Gets length of sources and their intersection
+                // For mRNA and GEM removes first element to not have in count the first column of the file (the index)
+                mRNAHeadersColumnsNames.shift()
+                clinicalHeadersColumnsNames.shift()
+
+                setForm(prevState => ({
+                    ...prevState,
+                    numberOfSamplesMRNA: mRNAHeadersColumnsNames.length,
+                    numberOfSamplesClinial: clinicalHeadersColumnsNames.length,
+                    numberOfSamplesInCommon: intersection(
+                        mRNAHeadersColumnsNames,
+                        clinicalHeadersColumnsNames
+                    ).length
+                }))
+            }).catch(errorReadingFileInInput)
+        }).catch(errorReadingFileInInput)
+    }
+
     return (
         <Segment className='diff--side--bar--container table-bordered'>
             <Header textAlign='center' className='margin-top-0'>
-                <Icon name='th' />
+                <Icon name='buromobelexperte' />
                 <Header.Content>New Differential Expression</Header.Content>
             </Header>
-            <Input
-                onChange={(e) => handleChangeForm(e.target.value, 'differentialExpressionName')}
-                type='text'
-                placeholder='Name'
-                className='diff--side--bar--container--item--margin'
-                value={form.differentialExpressionName}
-                icon='asterisk'
-            />
-
-            <TextArea
-                style={{ maxWidth: '100%', minWidth: '100%' }}
-                rows={3}
-                onChange={(_, e) => handleChangeForm(e.value ? e.value.toString() : '', 'differentialExpressionDescription')}
-                placeholder='Description'
-                className='diff--side--bar--container--item--margin'
-                value={form.differentialExpressionDescription}
-            />
-            {/* mRNA SourceForm */}
-            <SourceForm
-                source={form.mRNASource}
-                headerTitle='mRNA profile'
-                headerIcon={{
-                    type: 'img',
-                    src: 'static/frontend/img/profiles/mRNA.svg'
-                }}
-                fileType={FileType.MRNA}
-                disabled={form.isEditing}
-                tagOptions={[]}
-                handleChangeSourceType={(selectedSourceType) => {
-                    handleChangeSourceType(selectedSourceType, 'mRNASource')
-                }}
-                selectNewFile={selectNewFile}
-                selectUploadedFile={(selectedFile) => {
-                    selectUploadedFile(selectedFile, 'mRNASource')
-                }}
-                selectStudy={(selectedStudy) => {
-                    selectStudy(selectedStudy, 'mRNASource')
-                }}
-            />
-            {/* Clinical SourceForm */}
-            <SourceForm
-                source={form.clinicalSource}
-                headerTitle='Clinical profile'
-                headerIcon={{
-                    type: 'img',
-                    src: '/static/frontend/img/profiles/mRNA.svg'
-                }}
-                fileType={FileType.CLINICAL}
-                disabled={form.isEditing}
-                tagOptions={[]}
-                handleChangeSourceType={(selectedSourceType) => {
-                    handleChangeSourceType(selectedSourceType, 'clinicalSource')
-                }}
-                selectNewFile={selectNewFile}
-                selectUploadedFile={(selectedFile) => {
-                    selectUploadedFile(selectedFile, 'clinicalSource')
-                }}
-                selectStudy={(selectedStudy) => {
-                    selectStudy(selectedStudy, 'clinicalSource')
-                }}
-            />
-
-            <Form.Field width={6}>
-                <Label
-                    id='slider-cor-filter-label'
-                    className='align-center bolder'
-                >
-                    Percentile threshold {form.percentileThreshold.toFixed(2)}
-                </Label>
+            <Form>
+                <Form.Input
+                    onChange={(e) => handleChangeForm(e.target.value, 'differentialExpressionName')}
+                    type='text'
+                    placeholder='Name'
+                    className='diff--side--bar--container--item--margin'
+                    value={form.differentialExpressionName}
+                    icon='asterisk'
+                />
 
-                <SingleRangeSlider
-                    value={form.percentileThreshold}
-                    color='green'
-                    defaultMinValue={0}
-                    className='margin-bottom-5'
-                    defaultMaxValue={1}
-                    step={0.05}
-                    onChange={(value: number) => handleChangeForm(value, 'coefficientThreshold')}
+                <Form.TextArea
+                    style={{ maxWidth: '100%', minWidth: '100%' }}
+                    rows={3}
+                    onChange={(_, e) => handleChangeForm(e.value ? e.value.toString() : '', 'differentialExpressionDescription')}
+                    placeholder='Description'
+                    className='diff--side--bar--container--item--margin'
+                    value={form.differentialExpressionDescription}
                 />
+                {/* mRNA SourceForm */}
+                <Form.Field>
+                    <SourceForm
+                        source={form.mRNASource}
+                        headerTitle='mRNA profile'
+                        headerIcon={{
+                            type: 'img',
+                            src: 'static/frontend/img/profiles/mRNA.svg'
+                        }}
+                        fileType={FileType.MRNA}
+                        disabled={form.isEditing}
+                        tagOptions={[]}
+                        handleChangeSourceType={(selectedSourceType) => {
+                            handleChangeSourceType(selectedSourceType, 'mRNASource')
+                        }}
+                        selectNewFile={selectNewFile}
+                        selectUploadedFile={(selectedFile) => {
+                            selectUploadedFile(selectedFile, 'mRNASource')
+                        }}
+                        selectStudy={(selectedStudy) => {
+                            selectStudy(selectedStudy, 'mRNASource')
+                        }}
+                    />
+                </Form.Field>
+                {/* Clinical SourceForm */}
+                <Form.Field>
+                    <SourceForm
+                        source={form.clinicalSource}
+                        headerTitle='Clinical profile'
+                        headerIcon={{
+                            type: 'img',
+                            src: '/static/frontend/img/profiles/mRNA.svg'
+                        }}
+                        fileType={FileType.CLINICAL}
+                        disabled={form.isEditing}
+                        tagOptions={[]}
+                        handleChangeSourceType={(selectedSourceType) => {
+                            handleChangeSourceType(selectedSourceType, 'clinicalSource')
+                        }}
+                        selectNewFile={selectNewFile}
+                        selectUploadedFile={(selectedFile) => {
+                            selectUploadedFile(selectedFile, 'clinicalSource')
+                        }}
+                        selectStudy={(selectedStudy) => {
+                            selectStudy(selectedStudy, 'clinicalSource')
+                        }}
+                    />
+                </Form.Field>
+                <Form.Field>
+                    <Label className='full-width align-left'>
+                        <p>Samples mRNA: {form.numberOfSamplesMRNA}</p>
+                        <p>Samples clinical: {form.numberOfSamplesClinical}</p>
+                        <p>Samples in common: {form.numberOfSamplesInCommon}</p>
+                    </Label>
+                </Form.Field>
+                <Form.Field>
+                    <DifferentialExpressionInputClinicalAttribute
+                        optionsClinicalAttributes={form.optionsClinicalAttributes}
+                        clinicalAttribute={form.clinicalAttribute}
+                        onChange={(value: string) => handleChangeForm(value, 'clinicalAttribute')}
+                    />
+                </Form.Field>
+                {/* Coefficient threshold slider */}{/* Minimum Standard Deviation for Genes */}
+                <Form.Field className='diff--side--container--bar--slider'>
+                    <LabelWithInfoPopup
+                        labelText={`Threshold percentile: ${form.thresholdPercentile.toFixed(2)}`}
+                        popupContent='Percentile threshold for filtering low-expression genes (default 0.15)'
+                        centered
+                    />
+
+                    <SingleRangeSlider
+                        defaultMaxValue={1}
+                        defaultMinValue={0}
+                        step={0.05}
+                        value={form.thresholdPercentile}
+                        onChange={(value) => handleChangeForm(value, 'thresholdPercentile')}
+                        className='diff--side--bar--slider'
+                        color='blue'
+                    />
 
-                <Label
-                    id='label-minimum-threshold'
+                    <Label color='blue' className='pull-left'>0</Label>
+                    <Label color='blue' className='pull-right'>1</Label>
+                </Form.Field>
+                <Form.Field className='diff--side--container--bar--slider'>
+                    <LabelWithInfoPopup
+                        labelText={`Threshold std: ${toScientific(form.thresholdStd.toString())}`}
+                        popupContent='Variance threshold for gene filtering (default 1e-4)'
+                        centered
+                    />
+
+                    <SingleRangeSlider
+                        defaultMaxValue={0.01}
+                        defaultMinValue={0.0001}
+                        step={0.0001}
+                        value={form.thresholdStd}
+                        onChange={(value) => handleChangeForm(value, 'thresholdStd')}
+                        className='diff--side--bar--slider'
+                        color='blue'
+                    />
+
+                    <Label color='blue' className='pull-left'>1e-4</Label>
+                    <Label color='blue' className='pull-right'>1e-2</Label>
+                </Form.Field>
+                <Form.Field className='diff--side--container--bar--slider'>
+                    <LabelWithInfoPopup
+                        labelText={`Top: ${form.top}`}
+                        popupContent='Most significant number of genes to keep as result'
+                        centered
+                    />
+
+                    <SingleRangeSlider
+                        defaultMaxValue={1000}
+                        defaultMinValue={10}
+                        step={10}
+                        value={form.top}
+                        onChange={(value) => handleChangeForm(value, 'top')}
+                        className='diff--side--bar--slider'
+                        color='blue'
+                    />
+
+                    <Label color='blue' className='pull-left'>10</Label>
+                    <Label color='blue' className='pull-right'>1000</Label>
+                </Form.Field>
+
+                <Button
+                    type='submit'
+                    fluid
+                    primary
+                    className='margin-top-10'
+                    /*  disabled={(!formData.email.trim() && !formData.location.trim() && !formData.name.trim() && !formData.telephone_number.trim()) || formData.isLoading} */
+                    onClick={handleSubmit}
                     color='green'
-                    className='pull-left'
+                    loading={form.isLoading}
                 >
-                    {form.percentileThreshold.toFixed(2)}
-                </Label>
-                <Label color='green' className='pull-right'>1</Label>
-            </Form.Field>
+                    {form.isEditing ? 'Edit experiment' : 'Create experiment'}
+                </Button>
+            </Form>
+            <Button
+                className='margin-top-5'
+                fluid
+                primary
+                disabled={form.isLoading}
+                color='red'
+                onClick={() => setForm(cleanForm)}
+            >
+                {form.isEditing ? 'Cancel edit' : 'Reset form'}
+            </Button>
         </Segment>
     )
 }
+
+/**
+ * LabelWithInfoPopup's props
+ */
+interface LabelWithInfoPopupProps {
+    labelText: string,
+    popupContent: SemanticShorthandItem<PopupContentProps>,
+    centered?: boolean
+}
+
+/**
+ * Renders an label with an info popup. It's defined here for simplicity and reusability
+ * @param props Component's props
+ * @returns Component
+ */
+const LabelWithInfoPopup = (props: LabelWithInfoPopupProps) => (
+    <Label className={'full-width' + (props.centered ? ' align-center' : '')}>
+        {props.labelText}
+
+        <InfoPopup
+            content={props.popupContent}
+            onTop={false}
+            extraClassName='margin-left-2 no-margin-right pull-right'
+        />
+    </Label>
+)
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
new file mode 100644
index 00000000..3de92db1
--- /dev/null
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
@@ -0,0 +1,31 @@
+import React from 'react'
+import { Form } from 'semantic-ui-react'
+import { InputLabel } from '../common/InputLabel'
+
+interface DifferentialExpressionInputClinicalAttributeProps {
+    optionsClinicalAttributes: string[],
+    clinicalAttribute: string,
+    onChange: (value: string) => void,
+}
+
+export const DifferentialExpressionInputClinicalAttribute = (props: DifferentialExpressionInputClinicalAttributeProps) => {
+    return (
+        <>
+            <InputLabel label='Group by clinical attribute' />
+
+            <Form.Select
+                fluid
+                options={props.optionsClinicalAttributes.map((attr) => ({ key: attr, text: attr, value: attr }))}
+                loading={false}
+                className='margin-bottom-2'
+                search
+                selectOnBlur={false}
+                clearable
+                value={props.clinicalAttribute}
+                onChange={(_, { value }) => { props.onChange(value as string) }}
+                placeholder='Clinical attribute to group by'
+                disabled={false}
+            />
+        </>
+    )
+}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index 85792b56..4fa5ad6b 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -1,9 +1,30 @@
 import React from 'react'
 import { Base } from '../Base'
 import { DifferentialExpressionForm } from './DifferentialExpressionForm'
-import { Grid } from 'semantic-ui-react'
+import { DropdownItemProps, Grid, Table } from 'semantic-ui-react'
+import { PaginatedTable, PaginationCustomFilter } from '../common/PaginatedTable'
+import { TableCellWithTitle } from '../common/TableCellWithTitle'
+
+declare const urlDifferentialExpressionList:string
 
 export const DiferentialExpressionPanel = () => {
+    /**
+     * Generates default table's Filters.
+     * @returns Default object for table's Filters
+     */
+    const getDefaultFilters = (): PaginationCustomFilter[] => {
+        const tagOptions: DropdownItemProps[] = [{ id: 1, name: 'asd' }].map((tag) => {
+            const id = tag.id as number
+            return { key: id, value: id, text: tag.name }
+        })
+
+        tagOptions.unshift({ key: 'no_tag', text: 'No tag' })
+
+        return [
+            { label: 'Tag', keyForServer: 'tag', defaultValue: '', placeholder: 'Select an existing Tag', options: tagOptions, width: 3 }
+        ]
+    }
+
     return (
         <Base activeItem='differential-expression' wrapperClass='wrapper'>
             <Grid columns={2} padded stackable divided className='biomarkers--modal--container'>
@@ -13,7 +34,50 @@ export const DiferentialExpressionPanel = () => {
 
                 </Grid.Column>
                 <Grid.Column width={12}>
-
+                    <PaginatedTable<any>
+                        headerTitle='Biomarkers'
+                        headers={[
+                            { name: 'Name', serverCodeToSort: 'name', width: 3 },
+                            { name: 'Description', serverCodeToSort: 'description', width: 4 },
+                            { name: 'Tag', serverCodeToSort: 'tag' },
+                            { name: 'State', serverCodeToSort: 'state', textAlign: 'center' },
+                            { name: 'Origin', serverCodeToSort: 'origin', textAlign: 'center' },
+                            { name: 'Date', serverCodeToSort: 'upload_date' },
+                            { name: '# mRNAS', serverCodeToSort: 'number_of_mrnas', width: 1 },
+                            { name: '# miRNAS', serverCodeToSort: 'number_of_mirnas', width: 1 },
+                            { name: '# CNA', serverCodeToSort: 'number_of_cnas', width: 1 },
+                            { name: '# Methylation', serverCodeToSort: 'number_of_methylations', width: 1 },
+                            { name: 'Public', width: 1 },
+                            { name: 'Shared', width: 1 },
+                            { name: 'Actions', width: 2 }
+                        ]}
+                        defaultSortProp={{ sortField: 'upload_date', sortOrderAscendant: false }}
+                        customFilters={getDefaultFilters()}
+                        showSearchInput
+                        customElements={[
+                            /*  <Form.Field key={1} className='custom-table-field' title='Add new Biomarker'>
+                                <Button
+                                    primary
+                                    icon
+                                    onClick={() => this.setState({ formBiomarker: this.getDefaultFormBiomarker(), openCreateEditBiomarkerModal: true })}
+                                >
+                                    <Icon name='add' />
+                                </Button>
+                            </Form.Field> */
+                        ]}
+                        searchLabel='Name'
+                        searchPlaceholder='Search by name'
+                        urlToRetrieveData={urlDifferentialExpressionList}
+                        updateWSKey='update_biomarkers'
+                        mapFunction={(experiment: any) => {
+                            console.log(experiment)
+                            return (
+                                <Table.Row key={experiment.id as number}>
+                                    <TableCellWithTitle value={experiment.name} />
+                                </Table.Row>
+                            )
+                        }}
+                    />
                 </Grid.Column>
             </Grid>
         </Base>
diff --git a/src/frontend/static/frontend/src/css/differential-expression.css b/src/frontend/static/frontend/src/css/differential-expression.css
index 3314f289..3c92dd5f 100644
--- a/src/frontend/static/frontend/src/css/differential-expression.css
+++ b/src/frontend/static/frontend/src/css/differential-expression.css
@@ -7,4 +7,12 @@
 
 .diff--side--bar--container--item--margin {
     margin: 0.5rem 0;
+}
+.diff--side--container--bar--slider{
+    padding: 1rem 0;
+}
+.diff--side--bar--slider input{
+    width: 100%;
+    margin-top: 10px;
+    margin-bottom: 10px;
 }
\ No newline at end of file
diff --git a/src/frontend/static/frontend/src/utils/django_interfaces.ts b/src/frontend/static/frontend/src/utils/django_interfaces.ts
index 30ae349c..777b4ae5 100644
--- a/src/frontend/static/frontend/src/utils/django_interfaces.ts
+++ b/src/frontend/static/frontend/src/utils/django_interfaces.ts
@@ -355,6 +355,16 @@ interface DjangoSamplesInCommonResultJSON {
     number_samples_gem: number
 }
 
+/**
+ * JSON structure of the service that returns the number of samples in common between
+ * two datasets (UserFiles or CGDSDataset)
+ */
+interface DjangoSamplesInCommonResultMrnaClinicalJSON {
+    number_samples_in_common: number,
+    number_samples_mrna: number,
+    number_samples_clinical: number
+}
+
 /**
  * JSON structure of the service that returns the number of samples in common between
  * two datasets (UserFiles or CGDSDataset)
@@ -555,6 +565,13 @@ interface DjangoCommonResponse<INTERNAL_CODE_STATUS = null> {
     status: DjangoResponseStatus<INTERNAL_CODE_STATUS>
 }
 
+/**
+ * Django samples in common service Response
+ */
+interface DjangoNumberSamplesInCommonMrnaClinicalResult extends DjangoCommonResponse<DjangoSamplesInCommonResultInternalCode> {
+    data: DjangoSamplesInCommonResultMrnaClinicalJSON
+}
+
 /**
  * Django samples in common service Response
  */
@@ -719,5 +736,7 @@ export {
     DjangoInstitutionUser,
     DjangoInstitutionUserLimited,
     InstitutionUser,
-    DjangoUserSimple
+    DjangoUserSimple,
+    DjangoSamplesInCommonResultMrnaClinicalJSON,
+    DjangoNumberSamplesInCommonMrnaClinicalResult
 }
diff --git a/src/frontend/templates/frontend/differential-expression.html b/src/frontend/templates/frontend/differential-expression.html
index eb7f198e..2454263b 100644
--- a/src/frontend/templates/frontend/differential-expression.html
+++ b/src/frontend/templates/frontend/differential-expression.html
@@ -17,6 +17,9 @@
         <script>
             const urlDifferentialExpressionList = "{% url 'differential_expression_list' %}"
             const urlDifferentialExpressionSubmit = "{% url 'differential_expression_submit' %}"
+            const urlGetCommonSamplesDiferentialExperiment = "{% url 'get_common_samples_differential_experiment' %}"
+            const urlGetCommonSamplesOneFrontDiferentialExperiment = "{% url 'get_common_samples_one_front_differential_experiment' %}"
+            const urlGetClinicalAttributes = "{% url 'user_file_headers' %}"
         </script>
         {% render_bundle 'differentialExpression' 'js' %}
 {% endblock %}
\ No newline at end of file

From 37c08b49ee911668f45584d2bcd833cd89766437 Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Tue, 2 Sep 2025 20:22:46 -0300
Subject: [PATCH 11/47] fix list_of_samples

---
 src/differential_expression/views.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index c8335e19..06f18b56 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -427,6 +427,7 @@ def get(self, request: Request):
                     FileType.CLINICAL,
                     request.user
                 )
+                print(samples_list_mrna, samples_list_clinical)
                 intersection = get_intersection(samples_list_mrna, samples_list_clinical)
                 # Gets intersection
 
@@ -539,6 +540,9 @@ def get_samples_list(
 
             # Gets the corresponding Study's Dataset
             cgds_dataset = get_cgds_dataset(cgds_study, file_type)
+
+            list_of_samples = cgds_dataset.get_column_names()
+
         except CGDSDataset.DoesNotExist:
             response = {
                 'status': ResponseStatus(

From 6cc27f5af207cd901ca26d44ce948a634ccc7f1a Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Tue, 2 Sep 2025 22:58:44 -0300
Subject: [PATCH 12/47] base table + fix form

---
 .../DifferentialExpressionForm.tsx            |  34 ++-
 .../DifferentialExpressionPanel.tsx           | 195 ++++++++++++++++--
 .../differential-expression/types.ts          |  37 ++++
 3 files changed, 241 insertions(+), 25 deletions(-)
 create mode 100644 src/frontend/static/frontend/src/components/differential-expression/types.ts

diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
index df91a300..272afc53 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
@@ -2,13 +2,13 @@ import React, { useRef, useState } from 'react'
 import { Button, Form, Header, Icon, Label, PopupContentProps, Segment, SemanticShorthandItem } from 'semantic-ui-react'
 import { SourceForm } from '../pipeline/SourceForm'
 import { SingleRangeSlider } from 'neo-react-semantic-ui-range'
-import { FileType, KySearchParams, Nullable, Source, SourceType } from '../../utils/interfaces'
+import { CustomAlertTypes, FileType, KySearchParams, Nullable, Source, SourceType } from '../../utils/interfaces'
 import { cleanRef, getDefaultSource, getDjangoHeader, getFilenameFromSource, getFileSizeInMB, getInputFileCSVColumns } from '../../utils/util_functions'
 import { DjangoCGDSStudy, DjangoNumberSamplesInCommonMrnaClinicalResult, DjangoNumberSamplesInCommonOneFrontResult, DjangoResponseCode, DjangoUserFile } from '../../utils/django_interfaces'
 import { InfoPopup } from '../pipeline/experiment-result/gene-gem-details/InfoPopup'
 import ky from 'ky'
 import { MAX_FILE_SIZE_IN_MB_WARN } from '../../utils/constants'
-import { intersection } from 'lodash'
+import { intersection, isEqual } from 'lodash'
 import { DifferentialExpressionInputClinicalAttribute } from './DifferentialExpressionInputClinicalAttribute'
 
 // Define the possible field names for number of samples
@@ -67,8 +67,11 @@ const cleanForm: IDifferentialExpressionForm = {
     gettingCommonSamples: false,
     optionsClinicalAttributes: [],
 }
+interface DifferentialExpressionFormProps {
+    updateAlert: (type: CustomAlertTypes, msg: string) => void,
+}
 
-export const DifferentialExpressionForm = () => {
+export const DifferentialExpressionForm = (props: DifferentialExpressionFormProps) => {
     const [form, setForm] = useState<IDifferentialExpressionForm>(cleanForm)
     const abortController = useRef(new AbortController())
 
@@ -237,15 +240,20 @@ export const DifferentialExpressionForm = () => {
             thresholdPercentile: form.thresholdPercentile,
             threshold: form.thresholdStd,
             top: form.top,
+            clinicalCGDSStudyPk: form.clinicalSource.CGDSStudy?.id,
+            mRNACGDSStudyPk: form.mRNASource.CGDSStudy?.id,
+            clinicalExistingFilePk: form.clinicalSource.selectedExistingFile?.id,
+            mRNAExistingFilePk: form.mRNASource.selectedExistingFile?.id
         }
         ky.post(urlDifferentialExpressionSubmit, { headers: myHeaders, json: body }).then((response) => {
             response.json().then(() => {
-                console.log(response)
+                props.updateAlert(CustomAlertTypes.SUCCESS, 'Differential Expression experiment created successfully!')
             }).catch((err) => {
                 console.error('Error parsing JSON ->', err)
             })
         }).catch((err) => {
             console.error('Error getting users ->', err)
+            props.updateAlert(CustomAlertTypes.ERROR, 'Error creating Differential Expression experiment!')
         })
     }
 
@@ -274,8 +282,7 @@ export const DifferentialExpressionForm = () => {
      */
     const errorReadingFileInInput = (event) => {
         resetAllNumberOfSamples()
-        console.log('Error reading user\'s file')
-        console.log(event.target.error.name)
+        console.error('Error reading user\'s file', event.target.error.name)
     }
 
     /**
@@ -499,6 +506,17 @@ export const DifferentialExpressionForm = () => {
         }).catch(errorReadingFileInInput)
     }
 
+    /**
+     * Checks if the form can be submitted
+     * @returns True if the submit button is disabled.
+     */
+    const submitDisabled = (form.differentialExpressionName.trim() === '' ||
+            form.clinicalAttribute.trim() === '' ||
+            form.differentialExpressionDescription.trim() === '' ||
+            isEqual(form.mRNASource, () => getDefaultSource()) ||
+            isEqual(form.clinicalSource, () => getDefaultSource())
+    )
+
     return (
         <Segment className='diff--side--bar--container table-bordered'>
             <Header textAlign='center' className='margin-top-0'>
@@ -652,7 +670,7 @@ export const DifferentialExpressionForm = () => {
                     fluid
                     primary
                     className='margin-top-10'
-                    /*  disabled={(!formData.email.trim() && !formData.location.trim() && !formData.name.trim() && !formData.telephone_number.trim()) || formData.isLoading} */
+                    disabled={submitDisabled || form.isLoading}
                     onClick={handleSubmit}
                     color='green'
                     loading={form.isLoading}
@@ -664,7 +682,7 @@ export const DifferentialExpressionForm = () => {
                 className='margin-top-5'
                 fluid
                 primary
-                disabled={form.isLoading}
+                disabled={isEqual(form, cleanForm) || form.isLoading}
                 color='red'
                 onClick={() => setForm(cleanForm)}
             >
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index 4fa5ad6b..9c5c52fc 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -1,13 +1,64 @@
 import React from 'react'
 import { Base } from '../Base'
 import { DifferentialExpressionForm } from './DifferentialExpressionForm'
-import { DropdownItemProps, Grid, Table } from 'semantic-ui-react'
+import { DropdownItemProps, Grid, Icon, Table, TableCell } from 'semantic-ui-react'
 import { PaginatedTable, PaginationCustomFilter } from '../common/PaginatedTable'
 import { TableCellWithTitle } from '../common/TableCellWithTitle'
+import { Alert } from '../common/Alert'
+import { CustomAlert, CustomAlertTypes, GenesColors } from '../../utils/interfaces'
+import { DifferentialExpressionAnalysis, DifferentialExpressionAnalysisExperimentState } from './types'
+import { formatDateLocale, getExperimentStateObj } from '../../utils/util_functions'
+import { SourcePopup } from '../pipeline/all-experiments-view/SourcePopup'
+import { PopupIcons } from '../common/PopupIcons'
+import { DeleteButton } from '../common/DeleteButton'
+import { SwitchPublicButton } from '../common/SwitchPublicButton'
+import { StopExperimentButton } from '../pipeline/all-experiments-view/StopExperimentButton'
 
 declare const urlDifferentialExpressionList:string
 
 export const DiferentialExpressionPanel = () => {
+    /**
+     * Generates a default alert structure
+     * @returns Default the default Alert
+     */
+    const getDefaultAlertProps = (): CustomAlert => {
+        return {
+            message: '', // This have to change during cycle of component
+            isOpen: false,
+            type: CustomAlertTypes.SUCCESS,
+            duration: 500
+        }
+    }
+
+    const [state, setState] = React.useState({
+        alert: getDefaultAlertProps()
+    })
+
+    /**
+     * Reset the confirm modal, to be used again
+     */
+    const handleCloseAlert = () => {
+        setState(prevState => ({ ...prevState, alert: { ...prevState.alert, isOpen: false } }))
+    }
+
+    /**
+     * Updates the alert state to show a new alert
+     * @param type Type of alert
+     * @param msg Message to show in the alert
+     */
+    const updateAlert = (type: CustomAlertTypes, msg: string) => {
+        setState(prevState => ({
+            ...prevState,
+            alert: {
+                ...prevState.alert,
+                isOpen: true,
+                type,
+                message: msg,
+            }
+
+        }))
+    }
+
     /**
      * Generates default table's Filters.
      * @returns Default object for table's Filters
@@ -25,30 +76,38 @@ export const DiferentialExpressionPanel = () => {
         ]
     }
 
+    const confirmExperimentStop = (differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
+        // To implement
+        console.log(differentialExpressionAnalysis)
+    }
+
+    const confirmExperimentDeletion = (differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
+        // To implement
+        console.log(differentialExpressionAnalysis)
+    }
+
+    const handleChangeConfirmModalState = () => {
+        // To implement
+    }
+
     return (
         <Base activeItem='differential-expression' wrapperClass='wrapper'>
             <Grid columns={2} padded stackable divided className='biomarkers--modal--container'>
                 <Grid.Column width={4} textAlign='center'>
 
-                    <DifferentialExpressionForm />
+                    <DifferentialExpressionForm updateAlert={updateAlert} />
 
                 </Grid.Column>
                 <Grid.Column width={12}>
-                    <PaginatedTable<any>
-                        headerTitle='Biomarkers'
+                    <PaginatedTable<DifferentialExpressionAnalysis>
+                        headerTitle='Differential Expressions Analyses'
                         headers={[
                             { name: 'Name', serverCodeToSort: 'name', width: 3 },
                             { name: 'Description', serverCodeToSort: 'description', width: 4 },
-                            { name: 'Tag', serverCodeToSort: 'tag' },
-                            { name: 'State', serverCodeToSort: 'state', textAlign: 'center' },
-                            { name: 'Origin', serverCodeToSort: 'origin', textAlign: 'center' },
-                            { name: 'Date', serverCodeToSort: 'upload_date' },
-                            { name: '# mRNAS', serverCodeToSort: 'number_of_mrnas', width: 1 },
-                            { name: '# miRNAS', serverCodeToSort: 'number_of_mirnas', width: 1 },
-                            { name: '# CNA', serverCodeToSort: 'number_of_cnas', width: 1 },
-                            { name: '# Methylation', serverCodeToSort: 'number_of_methylations', width: 1 },
+                            { name: 'Date', serverCodeToSort: 'created_at' },
+                            { name: 'State', serverCodeToSort: 'state', width: 1, textAlign: 'center' },
+                            { name: 'Sources' },
                             { name: 'Public', width: 1 },
-                            { name: 'Shared', width: 1 },
                             { name: 'Actions', width: 2 }
                         ]}
                         defaultSortProp={{ sortField: 'upload_date', sortOrderAscendant: false }}
@@ -69,17 +128,119 @@ export const DiferentialExpressionPanel = () => {
                         searchPlaceholder='Search by name'
                         urlToRetrieveData={urlDifferentialExpressionList}
                         updateWSKey='update_biomarkers'
-                        mapFunction={(experiment: any) => {
-                            console.log(experiment)
+                        mapFunction={(differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
+                            console.log(differentialExpressionAnalysis)
+                            const isInProcess = differentialExpressionAnalysis.state === DifferentialExpressionAnalysisExperimentState.IN_PROCESS ||
+                            differentialExpressionAnalysis.state === DifferentialExpressionAnalysisExperimentState.WAITING_FOR_QUEUE
+
+                            const experimentState = getExperimentStateObj(differentialExpressionAnalysis.state as any)
+
                             return (
-                                <Table.Row key={experiment.id as number}>
-                                    <TableCellWithTitle value={experiment.name} />
+                                <Table.Row key={differentialExpressionAnalysis.id as number}>
+                                    <TableCellWithTitle value={differentialExpressionAnalysis.name} />
+                                    <TableCellWithTitle value={differentialExpressionAnalysis.description} />
+                                    <TableCellWithTitle value={formatDateLocale(differentialExpressionAnalysis.created_at as string, 'L')} />
+                                    <TableCell textAlign='center'>
+                                        <Icon
+                                            title={experimentState.title}
+                                            className={experimentState.className}
+                                            name={experimentState.iconName}
+                                            color={experimentState.color}
+                                            loading={experimentState.loading}
+                                        />
+                                    </TableCell>
+                                    <TableCell>
+                                        {/* Download mRNA */}
+                                        {/* <SourcePopup
+                                            source={differentialExpressionAnalysis.mrna_source}
+                                            iconName='file'
+                                            iconColor={GenesColors.MRNA}
+                                            downloadButtonTitle='Download source mRNA file'
+                                        />
+
+                                        <SourcePopup
+                                            source={differentialExpressionAnalysis.clinical_source}
+                                            iconName='file alternate'
+                                            iconColor={GenesColors.CLINICAL}
+                                            downloadButtonTitle='Download Clinical source file'
+                                        /> */}
+                                    </TableCell>
+                                    <TableCell textAlign='center'>
+                                        {
+                                            differentialExpressionAnalysis.is_public
+                                                ? (
+                                                    <Icon
+                                                        title='All users of the platform can see this experiment'
+                                                        name='check'
+                                                        color='green'
+                                                    />
+                                                )
+                                                : (
+                                                    <Icon
+                                                        title='If this is checked all the users in the platform can see (but not edit or remove) this element'
+                                                        name='close'
+                                                        color='red'
+                                                    />
+                                                )
+                                        }
+                                    </TableCell>
+                                    <TableCell>
+                                        {/* See results button */}
+
+                                        {/* Edit button */}
+                                        {/* <EditExperimentIcon
+                                            editExperiment={this.props.editExperiment}
+                                            experiment={experiment}
+                                            ownerId={experiment.user.id}
+                                        /> */}
+
+                                        <PopupIcons
+                                            content={(
+                                                <div style={{ display: 'flex', flexDirection: 'row', gap: '8px' }}>
+                                                    {/* Stop button */}
+                                                    <StopExperimentButton
+                                                        title='Stop experiment'
+                                                        onClick={() => confirmExperimentStop(differentialExpressionAnalysis)}
+                                                        ownerId={differentialExpressionAnalysis.user.id as number}
+                                                    />
+
+                                                    {/* Delete button */}
+                                                    {!isInProcess && !differentialExpressionAnalysis.is_public && (
+                                                        <DeleteButton
+                                                            title='Delete experiment'
+                                                            onClick={() => confirmExperimentDeletion(differentialExpressionAnalysis)}
+                                                            ownerId={differentialExpressionAnalysis.user.id}
+                                                        />
+                                                    )}
+
+                                                    {/* Public switch */}
+                                                    <SwitchPublicButton
+                                                        publicButtonEntity={{
+                                                            id: differentialExpressionAnalysis.id as number,
+                                                            user: { id: differentialExpressionAnalysis.user.id ?? 0 },
+                                                            is_public: differentialExpressionAnalysis.is_public
+                                                        }}
+                                                        publicKey='experimentId'
+                                                        nameEntity='experiment'
+                                                        handleChangeConfirmModalState={handleChangeConfirmModalState}
+                                                    />
+                                                </div>
+                                            )}
+                                        />
+                                    </TableCell>
                                 </Table.Row>
                             )
                         }}
                     />
                 </Grid.Column>
             </Grid>
+            <Alert
+                onClose={handleCloseAlert}
+                isOpen={state.alert.isOpen}
+                message={state.alert.message}
+                type={state.alert.type}
+                duration={state.alert.duration}
+            />
         </Base>
     )
 }
diff --git a/src/frontend/static/frontend/src/components/differential-expression/types.ts b/src/frontend/static/frontend/src/components/differential-expression/types.ts
new file mode 100644
index 00000000..71fd1050
--- /dev/null
+++ b/src/frontend/static/frontend/src/components/differential-expression/types.ts
@@ -0,0 +1,37 @@
+import { DjangoExperimentSource, DjangoUser } from '../../utils/django_interfaces'
+
+/**
+ * Possible states for experiment evaluation
+ */
+export enum DifferentialExpressionAnalysisExperimentState {
+    WAITING_FOR_QUEUE = 1,
+    IN_PROCESS = 2,
+    COMPLETED = 3,
+    FINISHED_WITH_ERROR = 4,
+    NO_SAMPLES_IN_COMMON = 5,
+    STOPPED = 7,
+    REACHED_ATTEMPTS_LIMIT = 8,
+    TIMEOUT_EXCEEDED = 9,
+}
+
+export interface DifferentialExpressionAnalysis {
+    id: number;
+    name: string;
+    description: string;
+    user: DjangoUser;
+    clinical_source: DjangoExperimentSource;
+    mrna_source: DjangoExperimentSource;
+    clinical_attribute: string;
+    threshold_percentile: number;
+    threshold: number;
+    top: number;
+    state: DifferentialExpressionAnalysisExperimentState;
+    state_display: string;
+    execution_time: number;
+    created_at: string;
+    updated_at: string;
+    is_public: boolean;
+    has_results: boolean;
+    results_count: number;
+    significant_genes_count: number;
+}

From ab8341c5d9da8e1aa151c67ffbcab42c5738b71e Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Mon, 8 Sep 2025 14:38:32 -0300
Subject: [PATCH 13/47] Implemented CGDS Dataset clinical attributes + Lot of
 formatting and refactoring

---
 README.md                                     |  2 +-
 src/datasets_synchronization/models.py        |  1 +
 src/datasets_synchronization/urls.py          |  3 +
 src/datasets_synchronization/views.py         | 15 ++++-
 src/differential_expression/views.py          | 63 ++++++++++---------
 .../frontend/differential-expression.html     |  1 +
 src/user_files/views.py                       | 41 ++++++------
 7 files changed, 74 insertions(+), 52 deletions(-)

diff --git a/README.md b/README.md
index ab7094cd..171a4801 100644
--- a/README.md
+++ b/README.md
@@ -15,7 +15,7 @@ This document is focused on the **development** of the system. If you are lookin
 - Node JS >= `20.x` (tested version: `20.x`)
 - [Modulector][modulector] `2.2.0`
 - [BioAPI][bioapi] `1.2.1`
-- R `4.4.2` (requerido para `differential-expression`)
+- R `4.4.2` (required for `differential-expression`)
 
 
 ## Installation 
diff --git a/src/datasets_synchronization/models.py b/src/datasets_synchronization/models.py
index ebf80f1d..8472f526 100644
--- a/src/datasets_synchronization/models.py
+++ b/src/datasets_synchronization/models.py
@@ -104,6 +104,7 @@ def __get_reverse_study(self) -> Optional['CGDSDataset']:
             return cast(Optional['CGDSDataset'], self.clinical_patient_dataset)
         elif hasattr(self, 'clinical_sample_dataset'):
             return cast(Optional['CGDSDataset'], self.clinical_sample_dataset)
+        return None
 
     @property
     def study(self) -> Optional['CGDSDataset']:
diff --git a/src/datasets_synchronization/urls.py b/src/datasets_synchronization/urls.py
index 595a6b54..9314e10a 100644
--- a/src/datasets_synchronization/urls.py
+++ b/src/datasets_synchronization/urls.py
@@ -7,6 +7,9 @@
     # CGDS Studies
     path('studies', views.CGDSStudyList.as_view(), name='cgds_studies'),
     path('studies/<int:pk>/', views.CGDSStudyDetail.as_view()),
+    # CGDS Datasets
+    path('cgds-dataset-clinical-attributes', views.CGDSDatasetClinicalAttributes.as_view(), name='cgds_dataset_clinical_attributes'),
+    path('cgds-dataset-clinical-attributes/<int:pk>/', views.CGDSDatasetClinicalAttributes.as_view()),
     # Synchronization
     path('sync', views.SyncCGDSStudy.as_view(), name='sync_cgds_study'),
     path('stop-sync', views.StopCGDSSync.as_view(), name='stop_cgds_study_sync')
diff --git a/src/datasets_synchronization/views.py b/src/datasets_synchronization/views.py
index 2818b2c6..8650bcc7 100644
--- a/src/datasets_synchronization/views.py
+++ b/src/datasets_synchronization/views.py
@@ -11,11 +11,11 @@
 from common.pagination import StandardResultsSetPagination
 from common.response import ResponseStatus
 from .enums import SyncCGDSStudyResponseCode, SyncStrategy
-from .models import CGDSStudy, CGDSDatasetSynchronizationState, CGDSStudySynchronizationState
+from .models import CGDSStudy, CGDSDatasetSynchronizationState, CGDSStudySynchronizationState, CGDSDataset
 from rest_framework import generics, permissions, filters
 from user_files.models_choices import FileType
 from .serializers import CGDSStudySerializer
-from django.shortcuts import render
+from django.shortcuts import render, get_object_or_404
 
 
 @login_required
@@ -214,3 +214,14 @@ def get(request: Request):
 
         # Formats to JSON the ResponseStatus object
         return Response(response)
+
+
+class CGDSDatasetClinicalAttributes(APIView):
+    """REST endpoint: list for CGDSDataset header."""
+    permission_classes = [permissions.IsAuthenticated]
+
+    @staticmethod
+    def get(request, pk: int):
+        """Gets the clinical attributes of a CGDSDataset."""
+        cgds_dataset: CGDSDataset = get_object_or_404(CGDSDataset, pk=pk)
+        return Response(cgds_dataset.get_column_names())
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 06f18b56..ffbb9ed4 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -1,8 +1,9 @@
-import json
+from typing import Optional, Dict, Tuple, List
 
+import numpy as np
+from celery.contrib.abortable import AbortableAsyncResult
 from django.db import transaction
 from django.db.models import Q
-
 from django_filters.rest_framework import DjangoFilterBackend
 from rest_framework import filters, generics, permissions
 from rest_framework.exceptions import ValidationError
@@ -13,13 +14,18 @@
 
 from api_service.enums import SourceType, CommonSamplesStatusErrorCode
 from api_service.utils import get_cgds_dataset
+from common.enums import ResponseCode
+from common.functions import get_enum_from_value, get_intersection, encode_json_response_status
 from common.pagination import StandardResultsSetPagination
+from common.response import ResponseStatus
+from datasets_synchronization.models import CGDSDataset
 from datasets_synchronization.models import CGDSStudy
 from differential_expression.models import (
     DifferentialExpressionClinicalSource,
     DifferentialExpressionExperiment,
     DifferentialExpressionSource,
 )
+from differential_expression.models import DifferentialExpressionExperimentState
 from differential_expression.serializers import (
     DifferentialExpressionExperimentDetailSerializer,
     DifferentialExpressionExperimentResultSerializer,
@@ -28,31 +34,24 @@
 from user_files.models import UserFile
 from user_files.models_choices import FileType
 from user_files.views import get_an_user_file
-
 from .tasks import eval_differential_expression_experiment
 
-from celery.contrib.abortable import AbortableAsyncResult
-from differential_expression.models import DifferentialExpressionExperimentState
-from common.functions import get_enum_from_value, get_intersection, encode_json_response_status
-from common.response import ResponseStatus
-from common.enums import ResponseCode
-from typing import Optional, Dict, Tuple, List, Type, OrderedDict, Union, cast, Any
-from datasets_synchronization.models import CGDSDataset
-
 
 def create_differential_expression_source(
-    source_type: int,
-    request: Request,
-    file_type: FileType,
-    prefix: str
-) -> tuple[DifferentialExpressionSource | DifferentialExpressionClinicalSource | None, DifferentialExpressionClinicalSource | None]:
+        source_type: int,
+        request: Request,
+        file_type: FileType,
+        prefix: str
+) -> tuple[
+    DifferentialExpressionSource | DifferentialExpressionClinicalSource | None, DifferentialExpressionClinicalSource | None
+]:
     """
     Creates a Source object for differential expression experiments.
     """
     is_clinical = prefix == 'clinical'
     source = DifferentialExpressionClinicalSource() if is_clinical else DifferentialExpressionSource()
     clinical_source = None
-    
+
     if source_type == SourceType.NEW_DATASET.value:
         # Adds a new User's file and uses it
         source_file = getattr(request, 'FILES', {}).get(f'{prefix}File')
@@ -69,16 +68,16 @@ def create_differential_expression_source(
         user_file.save()
         user_file.compute_post_saved_field()
         source.user_file = user_file
-        
+
     elif source_type == SourceType.CGDS.value:
         # Gets the CGDS Study
         post_data = getattr(request, 'data', {}) or getattr(request, 'POST', {})
         cgds_study_pk = post_data.get(f'{prefix}CGDSStudyPk')
         if not cgds_study_pk:
             return None, None
-            
+
         cgds_study = CGDSStudy.objects.get(pk=int(cgds_study_pk))
-        
+
         if is_clinical:
             # For clinical sources, we need both datasets
             if cgds_study.clinical_patient_dataset and cgds_study.clinical_sample_dataset:
@@ -92,14 +91,14 @@ def create_differential_expression_source(
                 source.cgds_dataset = cgds_dataset
             else:
                 return None, None
-        
+
     else:
         # Uses an existing User's file
         post_data = getattr(request, 'data', {}) or getattr(request, 'POST', {})
         existing_file_pk = post_data.get(f'{prefix}ExistingFilePk')
         if not existing_file_pk:
             return None, None
-            
+
         user_file = get_an_user_file(user=request.user, user_file_pk=int(existing_file_pk))
         source.user_file = user_file
 
@@ -150,7 +149,6 @@ def get_queryset(self):
             Q(shared_users=user)
         ).distinct()
 
-
         return experiments
 
     serializer_class = DifferentialExpressionExperimentSerializer
@@ -166,7 +164,8 @@ class DifferentialExpressionSubmit(APIView):
 
     permission_classes = [permissions.IsAuthenticated]
 
-    def post(self, request: Request):
+    @staticmethod
+    def post(request: Request):
         """
         Endpoint to submit a differential expression experiment.
         """
@@ -179,7 +178,6 @@ def post(self, request: Request):
 
             # Clinical source
             clinical_source_type = post_data.get('clinicalType')
-            print(clinical_source_type)
 
             if clinical_source_type:
                 clinical_source_type = int(clinical_source_type)
@@ -187,7 +185,6 @@ def post(self, request: Request):
                     clinical_source_type, request, FileType.CLINICAL, 'clinical')
                 # Select the valid one (if it's a CGDSStudy it needs clinical_aux as it has both needed CGDSDatasets)
                 clinical_source = clinical_aux if clinical_aux is not None else clinical_source
-                print(clinical_source, clinical_aux)
             else:
                 clinical_source = None
 
@@ -335,7 +332,8 @@ class DifferentialExpressionStop(APIView):
     """
     permission_classes = [permissions.IsAuthenticated]
 
-    def get(self, request: Request):
+    @staticmethod
+    def get(request: Request):
         experiment_id = request.GET.get('experimentId')
         if not experiment_id:
             raise ValidationError('experimentId is required.')
@@ -354,7 +352,7 @@ def get(self, request: Request):
                 experiment.shared_users.filter(id=user.id).exists()):
             raise ValidationError('You do not have permission to access this experiment.')
 
-        # Validaciones de estado y task
+        # Task state and validation
         if not experiment.task_id:
             return Response({'ok': False, 'detail': 'The experiment does not have an associated task.'})
 
@@ -383,6 +381,8 @@ def get(self, request: Request):
         experiment.save(update_fields=['state'])
 
         return Response({'ok': bool(aborted)})
+
+
 class GetCommonSamplesDifferentialExperiment(APIView):
     """Gets the number of in common samples between two datasets"""
 
@@ -427,7 +427,6 @@ def get(self, request: Request):
                     FileType.CLINICAL,
                     request.user
                 )
-                print(samples_list_mrna, samples_list_clinical)
                 intersection = get_intersection(samples_list_mrna, samples_list_clinical)
                 # Gets intersection
 
@@ -445,11 +444,13 @@ def get(self, request: Request):
         # Formats to JSON the ResponseStatus object
         return encode_json_response_status(response)
 
+
 class GetCommonSamplesDifferentialOneFrontExperiment(APIView):
     permission_classes = [permissions.IsAuthenticated]
     """Gets the number of in common samples between two datasets, one in the backend and other in the frontend"""
 
-    def post(self, request: Request):
+    @staticmethod
+    def post(request: Request):
         post_data = getattr(request, 'data', {}) or getattr(request, 'POST', {})
         headers_in_front: Optional[List[str]] = post_data.get('headersColumnsNames')
         other_source_id = post_data.get('otherSourceId')
@@ -493,6 +494,7 @@ def post(self, request: Request):
         # Formats to JSON the ResponseStatus object
         return encode_json_response_status(response)
 
+
 def get_samples_list(
         id_source: int,
         type_source: Optional[SourceType],
@@ -520,7 +522,6 @@ def get_samples_list(
     elif type_source == SourceType.UPLOADED_DATASETS:
         try:
             user_file = get_an_user_file(user=user, user_file_pk=id_source)
-            print(user_file)
             if file_type == FileType.CLINICAL:
                 list_of_samples = user_file.get_first_column_of_all_rows()
             else:
diff --git a/src/frontend/templates/frontend/differential-expression.html b/src/frontend/templates/frontend/differential-expression.html
index 2454263b..be437747 100644
--- a/src/frontend/templates/frontend/differential-expression.html
+++ b/src/frontend/templates/frontend/differential-expression.html
@@ -20,6 +20,7 @@
             const urlGetCommonSamplesDiferentialExperiment = "{% url 'get_common_samples_differential_experiment' %}"
             const urlGetCommonSamplesOneFrontDiferentialExperiment = "{% url 'get_common_samples_one_front_differential_experiment' %}"
             const urlGetClinicalAttributes = "{% url 'user_file_headers' %}"
+            const urlCGDSDatasetClinicalAttributes = "{% url 'cgds_dataset_clinical_attributes' %}"
         </script>
         {% render_bundle 'differentialExpression' 'js' %}
 {% endblock %}
\ No newline at end of file
diff --git a/src/user_files/views.py b/src/user_files/views.py
index e1549386..0535c2ea 100644
--- a/src/user_files/views.py
+++ b/src/user_files/views.py
@@ -43,7 +43,7 @@ def on_completion(self, uploaded_file: UploadedFile, request):
     def get_response_data(self, chunked_upload: ChunkedUpload, request):
         """Final response, returns the created UserFile object"""
         if self.raised_exception is None:
-            return { 'ok': True }
+            return {'ok': True}
 
         error_msg = self.raised_exception.detail['file_obj']['status']['message']
         return {
@@ -77,8 +77,8 @@ def get_own_or_as_admin_user_files(user: AbstractBaseUser):
     @return: User's Files
     """
     return UserFile.objects.filter(Q(user=user) | (
-        Q(institutions__institutionadministration__user=user)
-        & Q(institutions__institutionadministration__is_institution_admin=True)
+            Q(institutions__institutionadministration__user=user)
+            & Q(institutions__institutionadministration__is_institution_admin=True)
     )).distinct()
 
 
@@ -113,25 +113,28 @@ def get_user_files(user: AbstractBaseUser, public_only: bool, private_only: bool
 
     return user_files_objects.filter(filter_condition).select_related('tag').distinct()
 
+
 class UserFileHeaders(APIView):
     permission_classes = [permissions.IsAuthenticated]
     """REST endpoint: list for UserFile header. """
 
     @staticmethod
-    def get(request, pk: int) -> QuerySet:
+    def get(request, pk: int):
         """
-        Returns the User's files headers from DB
-        @param user: User to retrieve his Datasets
-        @param pk: Id from file
-        @return: File's headers
+        Returns the User's files headers from DB.
+        @param user: User to retrieve his Datasets.
+        @param pk: ID from file.
+        @return: File's headers.
         """
         user = request.user
         user_file = get_an_user_file(user=user, user_file_pk=pk)
         list_of_header = user_file.get_column_names()
         return Response(list_of_header)
 
+
 class UserFileList(generics.ListAPIView):
     """REST endpoint: list for UserFile model. """
+
     def get_queryset(self):
         # Returns own Datasets if explicitly requested...
         visibility = self.request.GET.get('visibility')
@@ -180,30 +183,32 @@ def get(request: HttpRequest, pk: Optional[int] = None):
 
         return response
 
+
 class ToggleFilePublicView(APIView):
     """
-    API endpoint to toggle the 'is_public' field of an a user file.
+    API endpoint to toggle the 'is_public' field of a UseFile.
     Only the owner of the user file can perform this action.
     """
     permission_classes = [permissions.IsAuthenticated]
 
-    def post(self, request):
+    @staticmethod
+    def post(request):
         """
         Toggle the 'is_public' field of the userFiles.
         """
         data = request.data
-       
-        userFile_id = data.get('userFileId')
-        userFile = get_object_or_404(UserFile, id=userFile_id)
-        if userFile.user.id != request.user.id:
+
+        user_file_id = data.get('userFileId')
+        user_file: UserFile = get_object_or_404(UserFile, id=user_file_id)
+        if user_file.user.id != request.user.id:
             return Response(
                 {"error": "You do not have permission to modify this user file."},
                 status=status.HTTP_403_FORBIDDEN
             )
 
-        userFile.is_public = not userFile.is_public
-        userFile.save(update_fields=['is_public'])  
+        user_file.is_public = not user_file.is_public
+        user_file.save(update_fields=['is_public'])
 
         return Response(
-            {"id": userFile.id, "is_public": userFile.is_public}
-        )
\ No newline at end of file
+            {"id": user_file.pk, "is_public": user_file.is_public}
+        )

From a6390c09fcd091f55c518b669beb2bcc1f06f9c5 Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Tue, 9 Sep 2025 08:19:57 -0300
Subject: [PATCH 14/47] save-9-9

---
 src/differential_expression/urls.py           |   1 +
 src/differential_expression/views.py          |  29 +++-
 .../DifferentialExpressionForm.tsx            |  22 ++-
 .../DifferentialExpressionPanel.tsx           | 149 +++++++++++++-----
 .../frontend/src/utils/util_functions.ts      |  32 +++-
 .../frontend/differential-expression.html     |   3 +
 src/user_files/views.py                       |   3 +
 7 files changed, 191 insertions(+), 48 deletions(-)

diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index 5b1f2b78..3bb174d3 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -10,4 +10,5 @@
     path('stop-experiment', views.DifferentialExpressionStop.as_view(), name='differential_expression_stop'),
     path('get-common-samples-differential-experiment', views.GetCommonSamplesDifferentialExperiment.as_view(), name='get_common_samples_differential_experiment'),
     path('get-common-samples-one-front-differential-experiment', views.GetCommonSamplesDifferentialOneFrontExperiment.as_view(), name='get_common_samples_one_front_differential_experiment'),
+    path('switch-institution-public-view', views.ToggleDiffExperimentPublicView.as_view(), name='switch-diff-experiment-public-view'),
     ]
\ No newline at end of file
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 06f18b56..ba306577 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -493,6 +493,34 @@ def post(self, request: Request):
         # Formats to JSON the ResponseStatus object
         return encode_json_response_status(response)
 
+class ToggleDiffExperimentPublicView(APIView):
+    """
+    API endpoint to toggle the 'is_public' field of an experiment.
+    Only the owner of the experiment can perform this action.
+    """
+    permission_classes = [permissions.IsAuthenticated]
+
+    def post(self, request):
+        """
+        Toggle the 'is_public' field of the experiment.
+        """
+        data = request.data
+        experiment_id = data.get('experimentId')
+        experiment = get_object_or_404(DifferentialExpressionExperiment, id=experiment_id)
+        if experiment.user.id != request.user.id:
+            return Response(
+                {"error": "You do not have permission to modify this experiment."},
+                status=status.HTTP_403_FORBIDDEN
+            )
+
+        experiment.is_public = not experiment.is_public
+        experiment.save(update_fields=['is_public'])
+
+        return Response(
+            {"id": experiment.id, "is_public": experiment.is_public}
+        )
+
+
 def get_samples_list(
         id_source: int,
         type_source: Optional[SourceType],
@@ -520,7 +548,6 @@ def get_samples_list(
     elif type_source == SourceType.UPLOADED_DATASETS:
         try:
             user_file = get_an_user_file(user=user, user_file_pk=id_source)
-            print(user_file)
             if file_type == FileType.CLINICAL:
                 list_of_samples = user_file.get_first_column_of_all_rows()
             else:
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
index 272afc53..8a7f508b 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
@@ -166,6 +166,8 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
      * and doesn't trigger an update of the state fields
      */
     const updateSourceFilenames = () => {
+        const updateClinicalAtt = getFilenameFromSource(form.clinicalSource) !== form.clinicalSource.filename
+
         setForm(prevState => ({
             ...prevState,
             clinicalSource: {
@@ -178,7 +180,10 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
             },
 
         }))
-        updateSelectClinicalAttribute()
+
+        if (updateClinicalAtt) {
+            updateSelectClinicalAttribute()
+        }
     }
 
     /**
@@ -194,9 +199,9 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
      * Callback when a new file is selected in the uncontrolled component
      * (input type=file)
      */
-    const selectNewFile = (e:any) => { 
-        console.log(e)
-        updateSourceFilenamesAndCommonSamples() }
+    const selectNewFile = () => {
+        updateSourceFilenamesAndCommonSamples()
+    }
 
     /**
      * change name or description of manual form
@@ -230,6 +235,10 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
     }
 
     const handleSubmit = () => {
+        setForm(prevState => ({
+            ...prevState,
+            isLoading: true
+        }))
         const myHeaders = getDjangoHeader()
         const body = {
             name: form.differentialExpressionName,
@@ -254,6 +263,11 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
         }).catch((err) => {
             console.error('Error getting users ->', err)
             props.updateAlert(CustomAlertTypes.ERROR, 'Error creating Differential Expression experiment!')
+        }).finally(() => {
+            setForm(prevState => ({
+                ...prevState,
+                isLoading: false
+            }))
         })
     }
 
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index 9c5c52fc..67ae61e8 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -1,37 +1,34 @@
-import React from 'react'
+import React, { useState } from 'react'
 import { Base } from '../Base'
 import { DifferentialExpressionForm } from './DifferentialExpressionForm'
-import { DropdownItemProps, Grid, Icon, Table, TableCell } from 'semantic-ui-react'
+import { Confirm, DropdownItemProps, Grid, Icon, Table, TableCell } from 'semantic-ui-react'
 import { PaginatedTable, PaginationCustomFilter } from '../common/PaginatedTable'
 import { TableCellWithTitle } from '../common/TableCellWithTitle'
 import { Alert } from '../common/Alert'
-import { CustomAlert, CustomAlertTypes, GenesColors } from '../../utils/interfaces'
+import { ConfirmModal, CustomAlert, CustomAlertTypes, GenesColors } from '../../utils/interfaces'
 import { DifferentialExpressionAnalysis, DifferentialExpressionAnalysisExperimentState } from './types'
-import { formatDateLocale, getExperimentStateObj } from '../../utils/util_functions'
+import { formatDateLocale, getDefaultAlertProps, getDefaultConfirmModal, getDjangoHeader, getExperimentStateObj } from '../../utils/util_functions'
 import { SourcePopup } from '../pipeline/all-experiments-view/SourcePopup'
 import { PopupIcons } from '../common/PopupIcons'
 import { DeleteButton } from '../common/DeleteButton'
 import { SwitchPublicButton } from '../common/SwitchPublicButton'
 import { StopExperimentButton } from '../pipeline/all-experiments-view/StopExperimentButton'
+import ky from 'ky'
 
 declare const urlDifferentialExpressionList:string
+declare const urlDifferentialExpressionStop:string
 
-export const DiferentialExpressionPanel = () => {
-    /**
-     * Generates a default alert structure
-     * @returns Default the default Alert
-     */
-    const getDefaultAlertProps = (): CustomAlert => {
-        return {
-            message: '', // This have to change during cycle of component
-            isOpen: false,
-            type: CustomAlertTypes.SUCCESS,
-            duration: 500
-        }
-    }
+interface DiferentialExpressionPanelState {
+    alert: CustomAlert
+    modal: ConfirmModal
+    stoppingExperiment: boolean
+}
 
-    const [state, setState] = React.useState({
-        alert: getDefaultAlertProps()
+export const DiferentialExpressionPanel = () => {
+    const [state, setState] = useState<DiferentialExpressionPanelState>({
+        alert: getDefaultAlertProps(),
+        modal: getDefaultConfirmModal(),
+        stoppingExperiment: false
     })
 
     /**
@@ -76,9 +73,25 @@ export const DiferentialExpressionPanel = () => {
         ]
     }
 
-    const confirmExperimentStop = (differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
-        // To implement
-        console.log(differentialExpressionAnalysis)
+    const confirmExperimentStop = (experimentId: number) => {
+        const myHeaders = getDjangoHeader()
+
+        ky.get(urlDifferentialExpressionStop, {
+            headers: myHeaders,
+            searchParams: { experimentId }
+        }).then((response) => {
+            // If OK closes the modal
+            if (response.ok) {
+                updateAlert(CustomAlertTypes.SUCCESS, 'Differential Expression experiment stopped successfully!')
+            } else {
+                updateAlert(CustomAlertTypes.ERROR, 'Error stopping Differential Expression experiment!')
+            }
+        }).catch((err) => {
+            updateAlert(CustomAlertTypes.ERROR, 'Error stopping Differential Expression experiment!')
+            console.error('Error stopping FSExperiment ->', err)
+        }).finally(() => {
+            setState(prevState => ({ ...prevState, stoppingExperiment: false }))
+        })
     }
 
     const confirmExperimentDeletion = (differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
@@ -86,8 +99,34 @@ export const DiferentialExpressionPanel = () => {
         console.log(differentialExpressionAnalysis)
     }
 
-    const handleChangeConfirmModalState = () => {
-        // To implement
+    /**
+     * Reset the confirm modal, to be used again
+     */
+    const handleCancelConfirmModalState = () => {
+        setState(prevState => ({
+            ...prevState,
+            modal: getDefaultConfirmModal()
+        }))
+    }
+
+    /**
+     * Changes confirm modal state
+     * @param setOption New state of option
+     * @param headerText Optional text of header in confirm modal, by default will be empty
+     * @param contentText optional text of content in confirm modal, by default will be empty
+     * @param onConfirm Modal onConfirm callback
+     */
+    const handleChangeConfirmModalState = (setOption: boolean, headerText: string, contentText: string, onConfirm: () => void) => {
+        setState(prevState => ({
+            ...prevState,
+            modal: {
+                ...prevState.modal,
+                confirmModal: setOption,
+                headerText,
+                contentText,
+                onConfirm
+            }
+        }))
     }
 
     return (
@@ -151,19 +190,26 @@ export const DiferentialExpressionPanel = () => {
                                     </TableCell>
                                     <TableCell>
                                         {/* Download mRNA */}
-                                        {/* <SourcePopup
-                                            source={differentialExpressionAnalysis.mrna_source}
-                                            iconName='file'
-                                            iconColor={GenesColors.MRNA}
-                                            downloadButtonTitle='Download source mRNA file'
-                                        />
+                                        {
+                                            differentialExpressionAnalysis.mrna_source.user_file && (
+                                                <>
+                                                    <SourcePopup
+                                                        source={differentialExpressionAnalysis.mrna_source}
+                                                        iconName='file'
+                                                        iconColor={GenesColors.MRNA}
+                                                        downloadButtonTitle='Download source mRNA file'
+                                                    />
+
+                                                    <SourcePopup
+                                                        source={differentialExpressionAnalysis.clinical_source}
+                                                        iconName='file alternate'
+                                                        iconColor={GenesColors.CLINICAL}
+                                                        downloadButtonTitle='Download Clinical source file'
+                                                    />
+                                                </>
+                                            )
+                                        }
 
-                                        <SourcePopup
-                                            source={differentialExpressionAnalysis.clinical_source}
-                                            iconName='file alternate'
-                                            iconColor={GenesColors.CLINICAL}
-                                            downloadButtonTitle='Download Clinical source file'
-                                        /> */}
                                     </TableCell>
                                     <TableCell textAlign='center'>
                                         {
@@ -198,11 +244,15 @@ export const DiferentialExpressionPanel = () => {
                                             content={(
                                                 <div style={{ display: 'flex', flexDirection: 'row', gap: '8px' }}>
                                                     {/* Stop button */}
-                                                    <StopExperimentButton
-                                                        title='Stop experiment'
-                                                        onClick={() => confirmExperimentStop(differentialExpressionAnalysis)}
-                                                        ownerId={differentialExpressionAnalysis.user.id as number}
-                                                    />
+                                                    {
+                                                        isInProcess && (
+                                                            <StopExperimentButton
+                                                                title='Stop experiment'
+                                                                onClick={() => handleChangeConfirmModalState(true, 'Stop Experiment', 'Are you sure to stop experiment?', () => confirmExperimentStop(differentialExpressionAnalysis.id))}
+                                                                ownerId={differentialExpressionAnalysis.user.id as number}
+                                                            />
+                                                        )
+                                                    }
 
                                                     {/* Delete button */}
                                                     {!isInProcess && !differentialExpressionAnalysis.is_public && (
@@ -241,6 +291,23 @@ export const DiferentialExpressionPanel = () => {
                 type={state.alert.type}
                 duration={state.alert.duration}
             />
+            <Confirm
+                open={state.modal.confirmModal}
+                header={state.modal.headerText}
+                content={state.modal.contentText}
+                size='large'
+                onCancel={() => handleCancelConfirmModalState()}
+                onConfirm={() => {
+                    state.modal.onConfirm()
+                    setState(prevState => ({
+                        ...prevState,
+                        modal: {
+                            ...prevState.modal,
+                            confirmModal: false
+                        }
+                    }))
+                }}
+            />
         </Base>
     )
 }
diff --git a/src/frontend/static/frontend/src/utils/util_functions.ts b/src/frontend/static/frontend/src/utils/util_functions.ts
index f09a9247..ad3f8c4b 100644
--- a/src/frontend/static/frontend/src/utils/util_functions.ts
+++ b/src/frontend/static/frontend/src/utils/util_functions.ts
@@ -1,5 +1,5 @@
 import React from 'react'
-import { FileType, StateIconInfo, GEMImageAndLabelInfo, CorrelationType, ExperimentResultTableControl, GeneralTableControl, Source, SourceType, HandleChangesCallback, Nullable, SortField, MirDIPScoreClass, ScoreClassData, BinData, ExperimentRequestPrefix } from './interfaces'
+import { FileType, StateIconInfo, GEMImageAndLabelInfo, CorrelationType, ExperimentResultTableControl, GeneralTableControl, Source, SourceType, HandleChangesCallback, Nullable, SortField, MirDIPScoreClass, ScoreClassData, BinData, ExperimentRequestPrefix, ConfirmModal, CustomAlert, CustomAlertTypes } from './interfaces'
 import { DropdownItemProps, InputOnChangeData } from 'semantic-ui-react'
 import { TagType, DjangoTag, ExperimentState, ExperimentType, CorrelationMethod, PValuesAdjustmentMethod, DjangoMRNAxGEMResultRow } from './django_interfaces'
 import dayjs from 'dayjs'
@@ -769,6 +769,32 @@ const getFileTypeName = (type: FileType): string => {
     return fileType
 }
 
+/**
+ * Generates a default confirm modal structure
+ * @returns Default confirmModal object
+ */
+const getDefaultConfirmModal = (): ConfirmModal => {
+    return {
+        confirmModal: false,
+        headerText: '',
+        contentText: '',
+        onConfirm: () => console.log('DefaultConfirmModalFunction, this should change during cycle of component')
+    }
+}
+
+/**
+ * Generates a default alert structure
+ * @returns Default the default Alert
+ */
+const getDefaultAlertProps = (): CustomAlert => {
+    return {
+        message: '', // This have to change during cycle of component
+        isOpen: false,
+        type: CustomAlertTypes.SUCCESS,
+        duration: 500
+    }
+}
+
 export {
     getDjangoHeader,
     alertGeneralError,
@@ -805,5 +831,7 @@ export {
     getScoreClassData,
     generateBinData,
     getFileTypeName,
-    getInputFileCSVFirstColumnAllRows
+    getInputFileCSVFirstColumnAllRows,
+    getDefaultConfirmModal,
+    getDefaultAlertProps
 }
diff --git a/src/frontend/templates/frontend/differential-expression.html b/src/frontend/templates/frontend/differential-expression.html
index 2454263b..3be0a47a 100644
--- a/src/frontend/templates/frontend/differential-expression.html
+++ b/src/frontend/templates/frontend/differential-expression.html
@@ -20,6 +20,9 @@
             const urlGetCommonSamplesDiferentialExperiment = "{% url 'get_common_samples_differential_experiment' %}"
             const urlGetCommonSamplesOneFrontDiferentialExperiment = "{% url 'get_common_samples_one_front_differential_experiment' %}"
             const urlGetClinicalAttributes = "{% url 'user_file_headers' %}"
+            const urlPostSwitchPublicView = "{% url 'switch-diff-experiment-public-view' %}"
+            const urlDifferentialExpressionStop = "{% url 'differential_expression_stop' %}"
+
         </script>
         {% render_bundle 'differentialExpression' 'js' %}
 {% endblock %}
\ No newline at end of file
diff --git a/src/user_files/views.py b/src/user_files/views.py
index e1549386..80253726 100644
--- a/src/user_files/views.py
+++ b/src/user_files/views.py
@@ -127,6 +127,9 @@ def get(request, pk: int) -> QuerySet:
         """
         user = request.user
         user_file = get_an_user_file(user=user, user_file_pk=pk)
+        """
+        
+        """
         list_of_header = user_file.get_column_names()
         return Response(list_of_header)
 

From 0ec3439d5d87e9926c9acbcb05a5a5f0a58c8681 Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Tue, 9 Sep 2025 08:27:31 -0300
Subject: [PATCH 15/47] fix select from save-9-9

---
 src/datasets_synchronization/urls.py                          | 2 +-
 .../differential-expression/DifferentialExpressionForm.tsx    | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/datasets_synchronization/urls.py b/src/datasets_synchronization/urls.py
index 9314e10a..e5f71a5d 100644
--- a/src/datasets_synchronization/urls.py
+++ b/src/datasets_synchronization/urls.py
@@ -8,7 +8,7 @@
     path('studies', views.CGDSStudyList.as_view(), name='cgds_studies'),
     path('studies/<int:pk>/', views.CGDSStudyDetail.as_view()),
     # CGDS Datasets
-    path('cgds-dataset-clinical-attributes', views.CGDSDatasetClinicalAttributes.as_view(), name='cgds_dataset_clinical_attributes'),
+    path('cgds-dataset-clinical-attributes/', views.CGDSDatasetClinicalAttributes.as_view(), name='cgds_dataset_clinical_attributes'),
     path('cgds-dataset-clinical-attributes/<int:pk>/', views.CGDSDatasetClinicalAttributes.as_view()),
     # Synchronization
     path('sync', views.SyncCGDSStudy.as_view(), name='sync_cgds_study'),
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
index 8a7f508b..7037d8f6 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
@@ -18,6 +18,7 @@ declare const urlDifferentialExpressionSubmit: string
 declare const urlGetCommonSamplesDiferentialExperiment: string
 declare const urlGetCommonSamplesOneFrontDiferentialExperiment: string
 declare const urlGetClinicalAttributes: string
+declare const urlCGDSDatasetClinicalAttributes: string
 
 /** Available types of Sources for a DifferentialExpressionForm. */
 type SourceStateDifferentialExpression = 'clinicalSource' | 'mRNASource'
@@ -146,7 +147,8 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
         } else if (form.clinicalSource.selectedExistingFile?.id || form.clinicalSource.CGDSStudy?.id) {
             const idToSearch = form.clinicalSource.selectedExistingFile?.id ?? form.clinicalSource.CGDSStudy?.id
             const myHeaders = getDjangoHeader()
-            ky.get(urlGetClinicalAttributes + `${idToSearch}/`, { timeout: 60000, headers: myHeaders, signal: abortController.current.signal }).then((response) => {
+            const url = form.clinicalSource.selectedExistingFile?.id ? urlGetClinicalAttributes + `${idToSearch}/` : urlCGDSDatasetClinicalAttributes + `${idToSearch}/`
+            ky.get(url, { timeout: 60000, headers: myHeaders, signal: abortController.current.signal }).then((response) => {
                 response.json().then((clinicalAttributes: string[]) => {
                     setForm(prevState => ({ ...prevState, optionsClinicalAttributes: clinicalAttributes }))
                 }).catch((err) => {

From b27c145df4c668c12492128bc5b4a1fc9c4785fd Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Mon, 15 Sep 2025 19:57:11 -0300
Subject: [PATCH 16/47] Add list serializer for differential expression
 experiments

Introduces DifferentialExpressionExperimentListSerializer to provide a lightweight representation for listing experiments, exposing only selected fields. Updates the DifferentialExpressionList view to use this new serializer for improved efficiency and clarity in API responses.
---
 src/differential_expression/models.py      | 12 +++----
 src/differential_expression/serializers.py | 37 ++++++++++++++++++++--
 src/differential_expression/views.py       |  5 +--
 3 files changed, 43 insertions(+), 11 deletions(-)

diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index 2439a57e..91ea02c7 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -15,17 +15,17 @@ class DifferentialExpressionSource(models.Model):
     A source could be a user file or a CGDS Dataset.
     """
     user_file = models.ForeignKey(
-        'user_files.UserFile', 
-        on_delete=models.CASCADE, 
-        blank=True, 
+        'user_files.UserFile',
+        on_delete=models.CASCADE,
+        blank=True,
         null=True,
         related_name='differential_expression_sources'
     )
     cgds_dataset = models.ForeignKey(
-        'datasets_synchronization.CGDSDataset', 
-        on_delete=models.CASCADE, 
+        'datasets_synchronization.CGDSDataset',
+        on_delete=models.CASCADE,
         blank=True,
-        null=True, 
+        null=True,
         related_name='differential_expression_sources'
     )
 
diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index 1d9ec685..6f378c6d 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -130,20 +130,51 @@ def get_is_significant(self, obj):
         return obj.adj_p_val <= 0.05 and abs(obj.log_fc) >= 1.0
 
 
+class DifferentialExpressionExperimentListSerializer(serializers.ModelSerializer):
+    """
+    Serializer para la lista general de experimentos de expresión diferencial.
+    Devuelve solo los campos solicitados: id, User, Name, Description, Date, State, Sources y si es publico.
+    """
+    # Sources - información de las fuentes de datos
+    clinical_source = DifferentialExpressionClinicalSourceSerializer(read_only=True)
+    mrna_source = DifferentialExpressionSourceSerializer(read_only=True)
+
+    # State information
+    state_display = serializers.CharField(source='get_state_display', read_only=True)
+
+    class Meta:
+        model = DifferentialExpressionExperiment
+        fields = [
+            'id',           # ID del experimento
+            'user',         # Información del usuario
+            'name',         # Nombre del experimento 
+            'description',  # Descripción del experimento
+            'created_at',   # Fecha de creación
+            'state',        # Estado del experimento
+            'state_display', # Estado legible
+            'clinical_source', # Fuente de datos clínicos
+            'mrna_source',     # Fuente de datos mRNA
+            'is_public'     # Si es público
+        ]
+        read_only_fields = [
+            'id', 'created_at', 'state', 'state_display'
+        ]
+
+
 class DifferentialExpressionExperimentSerializer(serializers.ModelSerializer):
     """
-    Serializer for Differential Expression Experiment (List view).
+    Serializer for Differential Expression Experiment (General view with all fields).
     """
     user = UserSimpleSerializer(read_only=True)
     clinical_source = DifferentialExpressionClinicalSourceSerializer(read_only=True)
     mrna_source = DifferentialExpressionSourceSerializer(read_only=True)
-    
+
     # Computed fields
     has_results = serializers.SerializerMethodField()
     results_count = serializers.SerializerMethodField()
     significant_genes_count = serializers.SerializerMethodField()
     state_display = serializers.CharField(source='get_state_display', read_only=True)
-    
+
     class Meta:
         model = DifferentialExpressionExperiment
         fields = [
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index d2ed2918..8afb49c7 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -29,7 +29,7 @@
 from differential_expression.serializers import (
     DifferentialExpressionExperimentDetailSerializer,
     DifferentialExpressionExperimentResultSerializer,
-    DifferentialExpressionExperimentSerializer,
+    DifferentialExpressionExperimentSerializer, DifferentialExpressionExperimentListSerializer,
 )
 from user_files.models import UserFile
 from user_files.models_choices import FileType
@@ -135,6 +135,7 @@ def get_object(self) -> DifferentialExpressionExperiment:
 class DifferentialExpressionList(generics.ListAPIView):
     """
     Endpoint to list all differential expression experiments.
+    Devuelve solo los campos: id, Name, Description, Date, State, Sources y si es publico.
     """
 
     def get_queryset(self):
@@ -151,7 +152,7 @@ def get_queryset(self):
 
         return experiments
 
-    serializer_class = DifferentialExpressionExperimentSerializer
+    serializer_class = DifferentialExpressionExperimentListSerializer
     permission_classes = [permissions.IsAuthenticated]
     pagination_class = StandardResultsSetPagination
     filter_backends = [filters.OrderingFilter, filters.SearchFilter, DjangoFilterBackend]

From ee95b9a7e1fed27699294dfa228c34b23c1530ca Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Thu, 18 Sep 2025 18:33:27 -0300
Subject: [PATCH 17/47] Add websocket updates for differential expression
 experiments

Introduces a websocket command and backend logic to notify the frontend when DifferentialExpressionExperiment instances are created, updated, or deleted. Refactors serializers to use shared ExperimentSource serializers for compatibility and updates the frontend to listen for the new websocket event key.
---
 src/api_service/websocket_functions.py        |  12 ++
 src/differential_expression/models.py         |  15 +++
 src/differential_expression/serializers.py    | 127 +++---------------
 .../DifferentialExpressionPanel.tsx           |   2 +-
 4 files changed, 49 insertions(+), 107 deletions(-)

diff --git a/src/api_service/websocket_functions.py b/src/api_service/websocket_functions.py
index 237e34b9..7825ec58 100644
--- a/src/api_service/websocket_functions.py
+++ b/src/api_service/websocket_functions.py
@@ -84,6 +84,18 @@ def send_update_trained_models_command(user_id: int):
     send_message(user_group_name, message)
 
 
+def send_update_differential_expression_experiments_command(user_id: int):
+    """
+    Sends a message indicating that a DifferentialExpressionExperiment state update has occurred
+    @param user_id: DifferentialExpressionExperiment's user's id to send the WS message
+    """
+    user_group_name = f'notifications_{user_id}'
+    message = {
+        'command': 'update_differential_expression_experiments'
+    }
+    send_message(user_group_name, message)
+
+
 def send_update_prediction_experiment_command(user_id: int):
     """
     Sends a message indicating that a InferenceExperiment state update has occurred
diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index 91ea02c7..ec8f68a1 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -7,6 +7,7 @@
 import numpy as np
 import math
 
+from api_service.websocket_functions import send_update_differential_expression_experiments_command
 from common.constants import PATIENT_ID_COLUMN
 
 class DifferentialExpressionSource(models.Model):
@@ -277,6 +278,7 @@ def __str__(self):
     def save(self, *args, **kwargs):
         """
         Override the save method to ensure that the name is unique.
+        Every time the experiment status changes, uses websockets to update state in the frontend.
         """
         if not self.name:
             raise ValueError("Experiment name cannot be empty.")
@@ -287,6 +289,9 @@ def save(self, *args, **kwargs):
 
         super().save(*args, **kwargs)
 
+        # Sends a websockets message to update the experiment state in the frontend
+        send_update_differential_expression_experiments_command(self.user.id)
+
     def save_results(self, dataframe):
         """
         Save the differential expression DataFrame results.
@@ -367,6 +372,16 @@ def get_significant_genes(self, p_value_threshold=0.05, log_fc_threshold=1.0):
             (Q(log_fc__gte=log_fc_threshold) | Q(log_fc__lte=-log_fc_threshold))
         )
 
+    def delete(self, *args, **kwargs):
+        """
+        Deletes the instance and sends a websockets message to update state in the frontend
+        """
+        user_id = self.user.id  # Store user_id before deletion
+        super().delete(*args, **kwargs)
+
+        # Sends a websockets message to update the experiment state in the frontend
+        send_update_differential_expression_experiments_command(user_id)
+
 
 class DifferentialExpressionExperimentResult(models.Model):
     """
diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index 6f378c6d..a32a0460 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -1,101 +1,14 @@
 from rest_framework import serializers
 from django.contrib.auth.models import User
 from institutions.models import Institution
+from api_service.serializers import ExperimentSourceSerializer, ExperimentClinicalSourceSerializer
 from differential_expression.models import (
-    DifferentialExpressionExperiment, 
+    DifferentialExpressionExperiment,
     DifferentialExpressionExperimentResult,
-    DifferentialExpressionSource,
     DifferentialExpressionClinicalSource
 )
 
 
-class DifferentialExpressionSourceSerializer(serializers.ModelSerializer):
-    """
-    Serializer for Differential Expression Source.
-    """
-    source_type = serializers.SerializerMethodField()
-    source_name = serializers.SerializerMethodField()
-    file_type = serializers.SerializerMethodField()
-    
-    class Meta:
-        model = DifferentialExpressionSource
-        fields = ['id', 'source_type', 'source_name', 'file_type', 'number_of_samples', 'number_of_rows']
-        read_only_fields = ['id', 'number_of_samples', 'number_of_rows']
-    
-    def get_source_type(self, obj):
-        """Returns the type of source."""
-        if obj.user_file:
-            return 'user_file'
-        elif obj.cgds_dataset:
-            return 'cgds_dataset'
-        return 'unknown'
-    
-    def get_source_name(self, obj):
-        """Returns the name of the source."""
-        try:
-            valid_source = obj.get_valid_source()
-            return getattr(valid_source, 'name', str(valid_source))
-        except:
-            return 'No source'
-    
-    def get_file_type(self, obj):
-        """Returns the file type of the source."""
-        try:
-            valid_source = obj.get_valid_source()
-            return getattr(valid_source, 'file_type', None)
-        except:
-            return None
-
-
-class DifferentialExpressionClinicalSourceSerializer(serializers.ModelSerializer):
-    """
-    Serializer for Differential Expression Clinical Source.
-    """
-    source_type = serializers.SerializerMethodField()
-    source_name = serializers.SerializerMethodField()
-    attributes_count = serializers.SerializerMethodField()
-    
-    class Meta:
-        model = DifferentialExpressionClinicalSource
-        fields = ['id', 'source_type', 'source_name', 'attributes_count', 'number_of_samples', 'number_of_rows']
-        read_only_fields = ['id', 'number_of_samples', 'number_of_rows']
-    
-    def get_source_type(self, obj):
-        """Returns the type of clinical source."""
-        if obj.user_file:
-            return 'user_file'
-        elif obj.cgds_dataset and obj.extra_cgds_dataset:
-            return 'cgds_clinical_combined'
-        elif obj.cgds_dataset:
-            return 'cgds_clinical'
-        return 'unknown'
-    
-    def get_source_name(self, obj):
-        """Returns the name of the clinical source."""
-        try:
-            if obj.user_file:
-                return obj.user_file.name
-            elif obj.cgds_dataset and obj.extra_cgds_dataset:
-                # For combined CGDS clinical sources, show both dataset names
-                main_name = str(obj.cgds_dataset)
-                extra_name = str(obj.extra_cgds_dataset)
-                return f"Clinical Combined: {main_name} + {extra_name}"
-            elif obj.cgds_dataset:
-                return str(obj.cgds_dataset)
-            return 'No source'
-        except Exception as e:
-            # More detailed error logging for debugging
-            import logging
-            logging.error(f"Error getting clinical source name: {e}")
-            return 'No source'
-    
-    def get_attributes_count(self, obj):
-        """Returns the number of clinical attributes."""
-        try:
-            return len(obj.get_attributes())
-        except:
-            return 0
-
 
 class UserSimpleSerializer(serializers.ModelSerializer):
     """Simple serializer for User model."""
@@ -132,12 +45,14 @@ def get_is_significant(self, obj):
 
 class DifferentialExpressionExperimentListSerializer(serializers.ModelSerializer):
     """
-    Serializer para la lista general de experimentos de expresión diferencial.
-    Devuelve solo los campos solicitados: id, User, Name, Description, Date, State, Sources y si es publico.
+    Optimized serializer for differential expression experiments list view.
+    Returns essential fields for table display: id, user, name, description, created_at,
+    state, clinical_source, mrna_source, and is_public.
+    Uses compatible source serializers that match frontend DjangoExperimentSource interface.
     """
-    # Sources - información de las fuentes de datos
-    clinical_source = DifferentialExpressionClinicalSourceSerializer(read_only=True)
-    mrna_source = DifferentialExpressionSourceSerializer(read_only=True)
+    # Sources - using standard API serializers compatible with frontend interfaces
+    clinical_source = ExperimentClinicalSourceSerializer(read_only=True)
+    mrna_source = ExperimentSourceSerializer(read_only=True)
 
     # State information
     state_display = serializers.CharField(source='get_state_display', read_only=True)
@@ -145,16 +60,16 @@ class DifferentialExpressionExperimentListSerializer(serializers.ModelSerializer
     class Meta:
         model = DifferentialExpressionExperiment
         fields = [
-            'id',           # ID del experimento
-            'user',         # Información del usuario
-            'name',         # Nombre del experimento 
-            'description',  # Descripción del experimento
-            'created_at',   # Fecha de creación
-            'state',        # Estado del experimento
-            'state_display', # Estado legible
-            'clinical_source', # Fuente de datos clínicos
-            'mrna_source',     # Fuente de datos mRNA
-            'is_public'     # Si es público
+            'id',              # Experiment ID
+            'user',            # User ID (compatible with frontend expectations)
+            'name',            # Experiment name
+            'description',     # Experiment description
+            'created_at',      # Creation date
+            'state',           # Experiment state
+            'state_display',   # Human-readable state
+            'clinical_source', # Clinical data source (ExperimentClinicalSourceSerializer)
+            'mrna_source',     # mRNA data source (ExperimentSourceSerializer)
+            'is_public'        # Public visibility flag
         ]
         read_only_fields = [
             'id', 'created_at', 'state', 'state_display'
@@ -166,8 +81,8 @@ class DifferentialExpressionExperimentSerializer(serializers.ModelSerializer):
     Serializer for Differential Expression Experiment (General view with all fields).
     """
     user = UserSimpleSerializer(read_only=True)
-    clinical_source = DifferentialExpressionClinicalSourceSerializer(read_only=True)
-    mrna_source = DifferentialExpressionSourceSerializer(read_only=True)
+    clinical_source = ExperimentClinicalSourceSerializer(read_only=True)
+    mrna_source = ExperimentSourceSerializer(read_only=True)
 
     # Computed fields
     has_results = serializers.SerializerMethodField()
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index 67ae61e8..7e50c6c8 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -166,7 +166,7 @@ export const DiferentialExpressionPanel = () => {
                         searchLabel='Name'
                         searchPlaceholder='Search by name'
                         urlToRetrieveData={urlDifferentialExpressionList}
-                        updateWSKey='update_biomarkers'
+                        updateWSKey='update_differential_expression_experiments'
                         mapFunction={(differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
                             console.log(differentialExpressionAnalysis)
                             const isInProcess = differentialExpressionAnalysis.state === DifferentialExpressionAnalysisExperimentState.IN_PROCESS ||

From 61c00566ceb89aabe374550228b4f6cdb5d2b575 Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Thu, 2 Oct 2025 19:53:33 -0300
Subject: [PATCH 18/47] Refactor significant genes endpoint into results view

Removed the DifferentialExpressionSignificantGenes endpoint and integrated its filtering logic into the DifferentialExpressionResults view. The results endpoint now supports filtering by p-value and fold-change thresholds via query parameters, simplifying the API and reducing redundancy.
---
 src/differential_expression/models.py |  2 +-
 src/differential_expression/urls.py   |  1 -
 src/differential_expression/views.py  | 57 ++++++++++-----------------
 3 files changed, 21 insertions(+), 39 deletions(-)

diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index ec8f68a1..88461bc2 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -6,6 +6,7 @@
 import pandas as pd
 import numpy as np
 import math
+from django.db.models import Q
 
 from api_service.websocket_functions import send_update_differential_expression_experiments_command
 from common.constants import PATIENT_ID_COLUMN
@@ -365,7 +366,6 @@ def get_significant_genes(self, p_value_threshold=0.05, log_fc_threshold=1.0):
         Returns:
             QuerySet: QuerySet of DifferentialExpressionExperimentResult objects meeting the criteria
         """
-        from django.db.models import Q
         
         return self.results.filter(
             Q(adj_p_val__lte=p_value_threshold) &
diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index 3bb174d3..7f01e392 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -5,7 +5,6 @@
     path('', views.DifferentialExpressionList.as_view(), name='differential_expression_list'),
     path('<int:pk>/', views.DifferentialExpressionDetail.as_view()),
     path('<int:pk>/results/', views.DifferentialExpressionResults.as_view()),
-    path('<int:pk>/significant-genes/', views.DifferentialExpressionSignificantGenes.as_view()),
     path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
     path('stop-experiment', views.DifferentialExpressionStop.as_view(), name='differential_expression_stop'),
     path('get-common-samples-differential-experiment', views.GetCommonSamplesDifferentialExperiment.as_view(), name='get_common_samples_differential_experiment'),
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 8afb49c7..259df75d 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -264,7 +264,8 @@ def post(request: Request):
 
 class DifferentialExpressionResults(generics.ListAPIView):
     """
-    Endpoint to get all results for a differential expression experiment.
+    Endpoint to get results for a differential expression experiment.
+    Supports filtering by p-value and fold-change thresholds via query parameters.
     """
     serializer_class = DifferentialExpressionExperimentResultSerializer
     permission_classes = [permissions.IsAuthenticated]
@@ -285,46 +286,28 @@ def get_queryset(self):
                 experiment.shared_users.filter(id=user.id).exists()):
             raise ValidationError('You do not have permission to access this experiment.')
 
-        return experiment.results.all()
+        # Get query parameters for filtering (optional)
+        p_threshold = self.request.query_params.get('p_threshold')
+        fc_threshold = self.request.query_params.get('fc_threshold')
 
+        # If filtering parameters are provided, apply filtering
+        if p_threshold is not None or fc_threshold is not None:
+            try:
+                p_threshold = float(p_threshold) if p_threshold is not None else 0.05
+                fc_threshold = float(fc_threshold) if fc_threshold is not None else 2.0
+            except ValueError as exc:
+                raise ValidationError('Invalid threshold values. Must be numeric.') from exc
 
-class DifferentialExpressionSignificantGenes(generics.ListAPIView):
-    """
-    Endpoint to get significant genes for a differential expression experiment.
-    """
-    serializer_class = DifferentialExpressionExperimentResultSerializer
-    permission_classes = [permissions.IsAuthenticated]
-    pagination_class = StandardResultsSetPagination
-    filter_backends = [filters.OrderingFilter]
-    ordering_fields = ['adj_p_val', 'log_fc', 'p_value', 'ave_expr']
-    ordering = ['adj_p_val']  # Default ordering by adjusted p-value
+            # Validate thresholds
+            if p_threshold < 0 or p_threshold > 1:
+                raise ValidationError('p_threshold must be between 0 and 1')
+            if fc_threshold < 0:
+                raise ValidationError('fc_threshold must be positive')
 
-    def get_queryset(self):
-        experiment_id = self.kwargs.get('pk')
-        experiment = get_object_or_404(DifferentialExpressionExperiment, pk=experiment_id)
-
-        # Check permissions (same logic as DifferentialExpressionDetail)
-        user = self.request.user
-        if not (experiment.is_public or
-                experiment.user == user or
-                experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
-                experiment.shared_users.filter(id=user.id).exists()):
-            raise ValidationError('You do not have permission to access this experiment.')
+            return experiment.get_significant_genes(p_threshold, fc_threshold)
 
-        # Get query parameters for filtering
-        try:
-            p_threshold = float(self.request.query_params.get('p_threshold', 0.05))
-            fc_threshold = float(self.request.query_params.get('fc_threshold', 2.0))
-        except ValueError as exc:
-            raise ValidationError('Invalid threshold values. Must be numeric.') from exc
-
-        # Validate thresholds
-        if p_threshold < 0 or p_threshold > 1:
-            raise ValidationError('p_threshold must be between 0 and 1')
-        if fc_threshold < 0:
-            raise ValidationError('fc_threshold must be positive')
-
-        return experiment.get_significant_genes(p_threshold, fc_threshold)
+        # Return all results if no filtering parameters
+        return experiment.results.all()
 
 
 class DifferentialExpressionStop(APIView):

From f7f6adb6d4fd36bd87f9a6c8255b3ade379f9a5f Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Thu, 2 Oct 2025 20:25:49 -0300
Subject: [PATCH 19/47] Add tool selection to DifferentialExpressionExperiment

Introduces a 'tool' field to DifferentialExpressionExperiment for specifying the analysis tool (DESEQ or LIMMA). Updates admin, model, serializer, and adds migration to support this new field. Removes significant genes count from admin display.
---
 src/differential_expression/admin.py          | 16 +++---------
 ...4_differentialexpressionexperiment_tool.py | 26 +++++++++++++++++++
 src/differential_expression/models.py         | 14 ++++++++++
 src/differential_expression/serializers.py    |  2 +-
 4 files changed, 45 insertions(+), 13 deletions(-)
 create mode 100644 src/differential_expression/migrations/0004_differentialexpressionexperiment_tool.py

diff --git a/src/differential_expression/admin.py b/src/differential_expression/admin.py
index 7ace471f..2481d57d 100644
--- a/src/differential_expression/admin.py
+++ b/src/differential_expression/admin.py
@@ -101,7 +101,7 @@ class DifferentialExpressionExperimentAdmin(admin.ModelAdmin):
     """Admin configuration for DifferentialExpressionExperiment model."""
     
     list_display = (
-        'id', 'name', 'user', 'state', 'clinical_attribute', 
+        'id', 'name', 'user', 'state', 'clinical_attribute', 'tool',
         'threshold_percentile', 'threshold', 'top', 'execution_time', 'created_at'
     )
     list_filter = (
@@ -110,7 +110,7 @@ class DifferentialExpressionExperimentAdmin(admin.ModelAdmin):
     search_fields = ('name', 'description', 'user__username', 'clinical_attribute')
     readonly_fields = (
         'id', 'task_id', 'execution_time', 'attempt', 'created_at', 'updated_at',
-        'get_results_count', 'get_significant_genes_count'
+        'get_results_count'
     )
     filter_horizontal = ('shared_institutions', 'shared_users')
     
@@ -122,14 +122,14 @@ class DifferentialExpressionExperimentAdmin(admin.ModelAdmin):
             'fields': ('clinical_source', 'mrna_source')
         }),
         ('Analysis Parameters', {
-            'fields': ('clinical_attribute', 'threshold_percentile', 'threshold', 'top')
+            'fields': ('clinical_attribute', 'tool', 'threshold_percentile', 'threshold', 'top')
         }),
         ('Execution Information', {
             'fields': ('state', 'task_id', 'execution_time', 'attempt', 'created_at', 'updated_at'),
             'classes': ('collapse',)
         }),
         ('Results Statistics', {
-            'fields': ('get_results_count', 'get_significant_genes_count'),
+            'fields': ('get_results_count',),
             'classes': ('collapse',)
         }),
         ('Sharing', {
@@ -145,14 +145,6 @@ def get_results_count(self, obj):
         except:
             return 0
     get_results_count.short_description = 'Total Results'
-    
-    def get_significant_genes_count(self, obj):
-        """Returns the number of significant genes with default thresholds."""
-        try:
-            return obj.get_significant_genes().count()
-        except:
-            return 0
-    get_significant_genes_count.short_description = 'Significant Genes (p<0.05, |logFC|>1)'
 
 
 @admin.register(DifferentialExpressionExperimentResult)
diff --git a/src/differential_expression/migrations/0004_differentialexpressionexperiment_tool.py b/src/differential_expression/migrations/0004_differentialexpressionexperiment_tool.py
new file mode 100644
index 00000000..a3925d57
--- /dev/null
+++ b/src/differential_expression/migrations/0004_differentialexpressionexperiment_tool.py
@@ -0,0 +1,26 @@
+# Generated by Django 4.2.19 on 2025-10-02 23:13
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "differential_expression",
+            "0003_differentialexpressionexperiment_top_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="differentialexpressionexperiment",
+            name="tool",
+            field=models.CharField(
+                choices=[("DESEQ", "Deseq"), ("LIMMA", "Limma")],
+                default="DESEQ",
+                help_text="Tool to use for differential expression analysis",
+                max_length=10,
+            ),
+        ),
+    ]
diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index 88461bc2..420a35f5 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -210,6 +210,11 @@ class DifferentialExpressionExperimentState(models.IntegerChoices):
     EMPTY_DATASET = 10
     TIMEOUT_EXCEEDED = 11
 
+class DifferentialExpressionTool(models.TextChoices):
+    """Tool choices for differential expression analysis."""
+    DESEQ = 'DESEQ'
+    LIMMA = 'LIMMA'
+
 class DifferentialExpressionExperiment(models.Model):
     """
     Model to create and manage differential expression data.
@@ -238,6 +243,15 @@ class DifferentialExpressionExperiment(models.Model):
 
     clinical_attribute = models.CharField(max_length=100, blank=False, null=False)
 
+    tool = models.CharField(
+        max_length=10,
+        choices=DifferentialExpressionTool.choices,
+        default=DifferentialExpressionTool.DESEQ,
+        blank=False,
+        null=False,
+        help_text='Tool to use for differential expression analysis'
+    )
+
     threshold_percentile = models.FloatField(default=0.15, blank=False, null=False)
 
     threshold = models.FloatField(default=0.0001, blank=False, null=False)
diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index a32a0460..bcddccc4 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -94,7 +94,7 @@ class Meta:
         model = DifferentialExpressionExperiment
         fields = [
             'id', 'name', 'description', 'user', 'clinical_source', 'mrna_source',
-            'clinical_attribute', 'threshold_percentile', 'threshold', 'top', 'state', 'state_display',
+            'clinical_attribute', 'tool', 'threshold_percentile', 'threshold', 'top', 'state', 'state_display',
             'execution_time', 'created_at', 'updated_at', 'is_public',
             'has_results', 'results_count', 'significant_genes_count'
         ]

From 2aa97eb474a885e932a9409bb4c1dad64eb5a0c0 Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Sat, 11 Oct 2025 12:03:35 -0300
Subject: [PATCH 20/47] Add tests and endpoints for experiment update and
 delete

Added comprehensive test coverage for differential expression experiment models, utilities, and views. Introduced API endpoints for updating and deleting experiments, including permission and state checks. Updated URL patterns to include new endpoints and added test data files for mRNA and clinical data.
---
 src/differential_expression/tests/__init__.py |   0
 .../tests/test_models.py                      | 294 +++++++
 .../tests/test_utils.py                       |  91 ++
 .../tests/test_views.py                       | 820 ++++++++++++++++++
 .../tests/tests_files/clinical_test.csv       |   5 +
 .../tests/tests_files/mrna_test.csv           |   6 +
 src/differential_expression/urls.py           |   2 +
 src/differential_expression/views.py          | 117 ++-
 8 files changed, 1334 insertions(+), 1 deletion(-)
 create mode 100644 src/differential_expression/tests/__init__.py
 create mode 100644 src/differential_expression/tests/test_models.py
 create mode 100644 src/differential_expression/tests/test_utils.py
 create mode 100644 src/differential_expression/tests/test_views.py
 create mode 100644 src/differential_expression/tests/tests_files/clinical_test.csv
 create mode 100644 src/differential_expression/tests/tests_files/mrna_test.csv

diff --git a/src/differential_expression/tests/__init__.py b/src/differential_expression/tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/differential_expression/tests/test_models.py b/src/differential_expression/tests/test_models.py
new file mode 100644
index 00000000..effd04b2
--- /dev/null
+++ b/src/differential_expression/tests/test_models.py
@@ -0,0 +1,294 @@
+from django.test import TestCase
+from django.contrib.auth.models import User
+from common.tests_utils import create_user_file
+from differential_expression.models import (
+    DifferentialExpressionExperiment,
+    DifferentialExpressionExperimentState,
+    DifferentialExpressionExperimentResult
+)
+from differential_expression.tests.test_utils import (
+    get_test_file_path,
+    create_differential_expression_source,
+    create_differential_expression_clinical_source,
+    create_test_differential_expression_experiment
+)
+from user_files.models_choices import FileType
+import pandas as pd
+
+
+class DifferentialExpressionExperimentModelTestCase(TestCase):
+    """Tests for DifferentialExpressionExperiment model"""
+
+    def setUp(self):
+        """Test setup"""
+        # Create test user
+        self.user = User.objects.create_user(
+            username='testuser',
+            email='test@test.com',
+            password='testpass123'
+        )
+
+        # Create test files
+        self.mrna_file = create_user_file(
+            get_test_file_path('mrna_test.csv'),
+            'mRNA Test',
+            FileType.MRNA,
+            self.user
+        )
+        self.clinical_file = create_user_file(
+            get_test_file_path('clinical_test.csv'),
+            'Clinical Test',
+            FileType.CLINICAL,
+            self.user
+        )
+
+        # Create sources
+        self.mrna_source = create_differential_expression_source(self.mrna_file)
+        self.clinical_source = create_differential_expression_clinical_source(self.clinical_file)
+
+    def test_create_experiment(self):
+        """Test creating a differential expression experiment"""
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user
+        )
+
+        self.assertIsNotNone(experiment.id)
+        self.assertEqual(experiment.name, 'Test Experiment')
+        self.assertEqual(experiment.state, DifferentialExpressionExperimentState.WAITING_FOR_QUEUE)
+        self.assertEqual(experiment.user, self.user)
+
+    def test_experiment_str_representation(self):
+        """Test string representation of experiment"""
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user
+        )
+
+        self.assertEqual(
+            str(experiment),
+            'Differential Expression Experiment: Test Experiment'
+        )
+
+    def test_experiment_default_values(self):
+        """Test experiment default values"""
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user
+        )
+
+        self.assertEqual(experiment.threshold_percentile, 0.15)
+        self.assertEqual(experiment.threshold, 0.0001)
+        self.assertEqual(experiment.top, 100)
+        self.assertEqual(experiment.attempt, 0)
+        self.assertEqual(experiment.execution_time, 0.0)
+        self.assertFalse(experiment.is_public)
+
+    def test_save_and_retrieve_results(self):
+        """Test saving and retrieving differential expression results"""
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Create test results dataframe
+        results_data = {
+            'AveExpr': [5.2, 6.1, 7.3],
+            'P.Value': [0.001, 0.05, 0.0001],
+            'adj.P.Val': [0.01, 0.1, 0.001],
+            'logFC': [2.5, -1.8, 3.2],
+            't': [4.5, -3.2, 5.1],
+            'B': [2.1, 1.5, 3.2]
+        }
+        results_df = pd.DataFrame(results_data, index=['GENE_1', 'GENE_2', 'GENE_3'])
+
+        # Save results
+        experiment.save_results(results_df)
+
+        # Retrieve results
+        retrieved_df = experiment.get_results_dataframe()
+
+        # Assert results were saved correctly
+        self.assertIsNotNone(retrieved_df)
+        self.assertEqual(len(retrieved_df), 3)
+        self.assertEqual(list(retrieved_df.index), ['GENE_1', 'GENE_2', 'GENE_3'])
+
+        # Check specific values
+        self.assertAlmostEqual(retrieved_df.loc['GENE_1', 'AveExpr'], 5.2, places=1)
+        self.assertAlmostEqual(retrieved_df.loc['GENE_1', 'logFC'], 2.5, places=1)
+
+    def test_get_significant_genes(self):
+        """Test getting significant genes"""
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Create test results
+        DifferentialExpressionExperimentResult.objects.create(
+            experiment=experiment,
+            gene='GENE_1',
+            ave_expr=5.2,
+            p_value=0.001,
+            adj_p_val=0.01,
+            log_fc=2.5,
+            t_statistic=4.5,
+            b_statistic=2.1
+        )
+        DifferentialExpressionExperimentResult.objects.create(
+            experiment=experiment,
+            gene='GENE_2',
+            ave_expr=6.1,
+            p_value=0.05,
+            adj_p_val=0.1,
+            log_fc=-0.5,
+            t_statistic=-1.2,
+            b_statistic=1.5
+        )
+        DifferentialExpressionExperimentResult.objects.create(
+            experiment=experiment,
+            gene='GENE_3',
+            ave_expr=7.3,
+            p_value=0.0001,
+            adj_p_val=0.001,
+            log_fc=3.2,
+            t_statistic=5.1,
+            b_statistic=3.2
+        )
+
+        # Get significant genes with default thresholds (p_value <= 0.05, |log_fc| >= 1.0)
+        significant_genes = experiment.get_significant_genes(
+            p_value_threshold=0.05,
+            log_fc_threshold=1.0
+        )
+
+        # Should return GENE_1 and GENE_3 (both have adj_p_val <= 0.05 and |log_fc| >= 1.0)
+        self.assertEqual(significant_genes.count(), 2)
+        gene_names = [result.gene for result in significant_genes]
+        self.assertIn('GENE_1', gene_names)
+        self.assertIn('GENE_3', gene_names)
+
+    def test_delete_experiment_cascades(self):
+        """Test that deleting experiment cascades to results"""
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Create test results
+        DifferentialExpressionExperimentResult.objects.create(
+            experiment=experiment,
+            gene='GENE_1',
+            ave_expr=5.2,
+            p_value=0.001,
+            adj_p_val=0.01,
+            log_fc=2.5,
+            t_statistic=4.5,
+            b_statistic=2.1
+        )
+
+        experiment_id = experiment.id
+
+        # Delete experiment
+        experiment.delete()
+
+        # Assert experiment and results were deleted
+        self.assertFalse(
+            DifferentialExpressionExperiment.objects.filter(pk=experiment_id).exists()
+        )
+        self.assertFalse(
+            DifferentialExpressionExperimentResult.objects.filter(
+                experiment_id=experiment_id
+            ).exists()
+        )
+
+
+class DifferentialExpressionSourceModelTestCase(TestCase):
+    """Tests for DifferentialExpressionSource models"""
+
+    def setUp(self):
+        """Test setup"""
+        # Create test user
+        self.user = User.objects.create_user(
+            username='testuser',
+            email='test@test.com',
+            password='testpass123'
+        )
+
+        # Create test files
+        self.mrna_file = create_user_file(
+            get_test_file_path('mrna_test.csv'),
+            'mRNA Test',
+            FileType.MRNA,
+            self.user
+        )
+        self.clinical_file = create_user_file(
+            get_test_file_path('clinical_test.csv'),
+            'Clinical Test',
+            FileType.CLINICAL,
+            self.user
+        )
+
+    def test_create_mrna_source(self):
+        """Test creating an mRNA source"""
+        source = create_differential_expression_source(self.mrna_file)
+
+        self.assertIsNotNone(source.id)
+        self.assertEqual(source.user_file, self.mrna_file)
+
+    def test_create_clinical_source(self):
+        """Test creating a clinical source"""
+        source = create_differential_expression_clinical_source(self.clinical_file)
+
+        self.assertIsNotNone(source.id)
+        self.assertEqual(source.user_file, self.clinical_file)
+
+    def test_get_samples_from_mrna_source(self):
+        """Test getting samples from mRNA source"""
+        source = create_differential_expression_source(self.mrna_file)
+
+        samples = source.get_samples()
+
+        # Based on mrna_test.csv
+        self.assertEqual(len(samples), 5)
+        self.assertIn('SAMPLE_1', samples)
+        self.assertIn('SAMPLE_5', samples)
+
+    def test_get_samples_from_clinical_source(self):
+        """Test getting samples from clinical source"""
+        source = create_differential_expression_clinical_source(self.clinical_file)
+
+        samples = source.get_samples()
+
+        # Based on clinical_test.csv
+        self.assertEqual(len(samples), 5)
+        self.assertIn('SAMPLE_1', samples)
+        self.assertIn('SAMPLE_5', samples)
+
+    def test_get_clinical_attributes(self):
+        """Test getting clinical attributes"""
+        source = create_differential_expression_clinical_source(self.clinical_file)
+
+        attributes = source.get_attributes()
+
+        # Based on clinical_test.csv (AGE, GENDER, STATUS, STAGE)
+        self.assertEqual(len(attributes), 4)
+        self.assertIn('AGE', attributes)
+        self.assertIn('GENDER', attributes)
+        self.assertIn('STATUS', attributes)
+        self.assertIn('STAGE', attributes)
diff --git a/src/differential_expression/tests/test_utils.py b/src/differential_expression/tests/test_utils.py
new file mode 100644
index 00000000..56c9eb1b
--- /dev/null
+++ b/src/differential_expression/tests/test_utils.py
@@ -0,0 +1,91 @@
+import os
+from typing import Optional
+from django.contrib.auth.models import User
+from common.tests_utils import create_user_file
+from differential_expression.models import (
+    DifferentialExpressionSource,
+    DifferentialExpressionClinicalSource,
+    DifferentialExpressionExperiment,
+    DifferentialExpressionExperimentState,
+    DifferentialExpressionTool
+)
+from user_files.models import UserFile
+from user_files.models_choices import FileType
+
+
+def get_test_file_path(filename: str) -> str:
+    """
+    Gets the absolute file's path in test folder
+    @param filename: File's name
+    @return: Absolute path to the file in test folder
+    """
+    dir_name = os.path.dirname(__file__)
+    file_path = os.path.join(dir_name, f'tests_files/{filename}')
+    return file_path
+
+
+def create_differential_expression_source(user_file: UserFile) -> DifferentialExpressionSource:
+    """
+    Creates a new instance of DifferentialExpressionSource saved in DB
+    @param user_file: UserFile to create the DifferentialExpressionSource
+    @return: DifferentialExpressionSource saved instance
+    """
+    source = DifferentialExpressionSource.objects.create(user_file=user_file)
+    return source
+
+
+def create_differential_expression_clinical_source(user_file: UserFile) -> DifferentialExpressionClinicalSource:
+    """
+    Creates a new instance of DifferentialExpressionClinicalSource saved in DB
+    @param user_file: UserFile to create the DifferentialExpressionClinicalSource
+    @return: DifferentialExpressionClinicalSource saved instance
+    """
+    source = DifferentialExpressionClinicalSource.objects.create(user_file=user_file)
+    return source
+
+
+def create_test_differential_expression_experiment(
+        name: str,
+        clinical_source: DifferentialExpressionClinicalSource,
+        mrna_source: DifferentialExpressionSource,
+        user: User,
+        state: DifferentialExpressionExperimentState = DifferentialExpressionExperimentState.WAITING_FOR_QUEUE,
+        description: str = 'Test experiment',
+        clinical_attribute: str = 'STATUS',
+        tool: DifferentialExpressionTool = DifferentialExpressionTool.DESEQ,
+        threshold_percentile: float = 0.15,
+        threshold: float = 0.0001,
+        top: int = 100,
+        task_id: Optional[str] = None
+) -> DifferentialExpressionExperiment:
+    """
+    Create a test DifferentialExpressionExperiment object
+    @param name: Experiment name
+    @param clinical_source: Clinical data source
+    @param mrna_source: mRNA data source
+    @param user: User who owns the experiment
+    @param state: Initial experiment state
+    @param description: Experiment description
+    @param clinical_attribute: Clinical attribute to use for analysis
+    @param tool: Tool to use for differential expression analysis
+    @param threshold_percentile: Threshold percentile for filtering
+    @param threshold: Threshold for filtering
+    @param top: Number of top results to keep
+    @param task_id: Optional Celery task ID
+    @return: Saved DifferentialExpressionExperiment instance
+    """
+    experiment = DifferentialExpressionExperiment.objects.create(
+        name=name,
+        description=description,
+        clinical_source=clinical_source,
+        mrna_source=mrna_source,
+        clinical_attribute=clinical_attribute,
+        tool=tool,
+        threshold_percentile=threshold_percentile,
+        threshold=threshold,
+        top=top,
+        state=state,
+        user=user,
+        task_id=task_id
+    )
+    return experiment
diff --git a/src/differential_expression/tests/test_views.py b/src/differential_expression/tests/test_views.py
new file mode 100644
index 00000000..4b9fbece
--- /dev/null
+++ b/src/differential_expression/tests/test_views.py
@@ -0,0 +1,820 @@
+from django.test import TestCase
+from django.contrib.auth.models import User
+from rest_framework.test import APIClient
+from rest_framework import status
+from unittest.mock import patch, MagicMock
+from common.tests_utils import create_user_file
+from differential_expression.models import (
+    DifferentialExpressionExperiment,
+    DifferentialExpressionExperimentState
+)
+from differential_expression.tests.test_utils import (
+    get_test_file_path,
+    create_differential_expression_source,
+    create_differential_expression_clinical_source,
+    create_test_differential_expression_experiment
+)
+from user_files.models_choices import FileType
+
+
+class DifferentialExpressionDeleteTestCase(TestCase):
+    """Tests for DifferentialExpressionDelete endpoint"""
+
+    def setUp(self):
+        """Test setup"""
+        # Create test users
+        self.owner = User.objects.create_user(
+            username='owner',
+            email='owner@test.com',
+            password='testpass123'
+        )
+        self.other_user = User.objects.create_user(
+            username='other',
+            email='other@test.com',
+            password='testpass123'
+        )
+
+        # Create test files
+        self.mrna_file = create_user_file(
+            get_test_file_path('mrna_test.csv'),
+            'mRNA Test',
+            FileType.MRNA,
+            self.owner
+        )
+        self.clinical_file = create_user_file(
+            get_test_file_path('clinical_test.csv'),
+            'Clinical Test',
+            FileType.CLINICAL,
+            self.owner
+        )
+
+        # Create sources
+        self.mrna_source = create_differential_expression_source(self.mrna_file)
+        self.clinical_source = create_differential_expression_clinical_source(self.clinical_file)
+
+        # Create API client
+        self.client = APIClient()
+
+    def test_delete_experiment_success(self):
+        """Test successfully deleting a completed experiment"""
+        # Create a completed experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Delete the experiment
+        url = f'/differential-expression/{experiment.pk}/delete'
+        response = self.client.delete(url)
+
+        # Assert response
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertTrue(response.data['ok'])
+
+        # Assert experiment was deleted
+        self.assertFalse(
+            DifferentialExpressionExperiment.objects.filter(pk=experiment.pk).exists()
+        )
+
+    def test_delete_experiment_not_owner(self):
+        """Test that non-owner cannot delete experiment"""
+        # Create experiment owned by owner
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Authenticate as other user
+        self.client.force_authenticate(user=self.other_user)
+
+        # Try to delete the experiment
+        url = f'/differential-expression/{experiment.pk}/delete'
+        response = self.client.delete(url)
+
+        # Assert forbidden
+        self.assertEqual(response.status_code, status.HTTP_403_FORBIDDEN)
+        self.assertFalse(response.data['ok'])
+
+        # Assert experiment still exists
+        self.assertTrue(
+            DifferentialExpressionExperiment.objects.filter(pk=experiment.pk).exists()
+        )
+
+    def test_delete_experiment_running_in_process(self):
+        """Test that running experiment cannot be deleted"""
+        # Create a running experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Running Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.IN_PROCESS,
+            task_id='test-task-id'
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Try to delete the experiment
+        url = f'/differential-expression/{experiment.pk}/delete'
+        response = self.client.delete(url)
+
+        # Assert bad request
+        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
+        self.assertFalse(response.data['ok'])
+        self.assertIn('running', response.data['detail'].lower())
+
+        # Assert experiment still exists
+        self.assertTrue(
+            DifferentialExpressionExperiment.objects.filter(pk=experiment.pk).exists()
+        )
+
+    def test_delete_experiment_waiting_for_queue(self):
+        """Test that experiment waiting for queue cannot be deleted"""
+        # Create experiment waiting for queue
+        experiment = create_test_differential_expression_experiment(
+            name='Waiting Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.WAITING_FOR_QUEUE,
+            task_id='test-task-id'
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Try to delete the experiment
+        url = f'/differential-expression/{experiment.pk}/delete'
+        response = self.client.delete(url)
+
+        # Assert bad request
+        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
+        self.assertFalse(response.data['ok'])
+
+        # Assert experiment still exists
+        self.assertTrue(
+            DifferentialExpressionExperiment.objects.filter(pk=experiment.pk).exists()
+        )
+
+    def test_delete_experiment_stopping(self):
+        """Test that experiment being stopped cannot be deleted"""
+        # Create experiment being stopped
+        experiment = create_test_differential_expression_experiment(
+            name='Stopping Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.STOPPING,
+            task_id='test-task-id'
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Try to delete the experiment
+        url = f'/differential-expression/{experiment.pk}/delete'
+        response = self.client.delete(url)
+
+        # Assert bad request
+        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
+        self.assertFalse(response.data['ok'])
+
+        # Assert experiment still exists
+        self.assertTrue(
+            DifferentialExpressionExperiment.objects.filter(pk=experiment.pk).exists()
+        )
+
+    def test_delete_experiment_stopped_success(self):
+        """Test that stopped experiment can be deleted"""
+        # Create stopped experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Stopped Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.STOPPED
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Delete the experiment
+        url = f'/differential-expression/{experiment.pk}/delete'
+        response = self.client.delete(url)
+
+        # Assert success
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertTrue(response.data['ok'])
+
+        # Assert experiment was deleted
+        self.assertFalse(
+            DifferentialExpressionExperiment.objects.filter(pk=experiment.pk).exists()
+        )
+
+    def test_delete_experiment_with_error_success(self):
+        """Test that experiment with error can be deleted"""
+        # Create experiment with error
+        experiment = create_test_differential_expression_experiment(
+            name='Error Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.FINISHED_WITH_ERROR
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Delete the experiment
+        url = f'/differential-expression/{experiment.pk}/delete'
+        response = self.client.delete(url)
+
+        # Assert success
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertTrue(response.data['ok'])
+
+        # Assert experiment was deleted
+        self.assertFalse(
+            DifferentialExpressionExperiment.objects.filter(pk=experiment.pk).exists()
+        )
+
+    def test_delete_experiment_not_authenticated(self):
+        """Test that unauthenticated user cannot delete experiment"""
+        # Create experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Don't authenticate
+
+        # Try to delete the experiment
+        url = f'/differential-expression/{experiment.pk}/delete'
+        response = self.client.delete(url)
+
+        # Assert unauthorized
+        self.assertEqual(response.status_code, status.HTTP_401_UNAUTHORIZED)
+
+        # Assert experiment still exists
+        self.assertTrue(
+            DifferentialExpressionExperiment.objects.filter(pk=experiment.pk).exists()
+        )
+
+    def test_delete_experiment_not_found(self):
+        """Test deleting non-existent experiment returns 404"""
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Try to delete non-existent experiment
+        url = '/differential-expression/99999/delete'
+        response = self.client.delete(url)
+
+        # Assert not found
+        self.assertEqual(response.status_code, status.HTTP_404_NOT_FOUND)
+
+    @patch('differential_expression.views.AbortableAsyncResult')
+    def test_delete_experiment_with_active_task(self, mock_async_result):
+        """Test that experiment with active Celery task gets aborted before deletion"""
+        # Mock the AbortableAsyncResult
+        mock_result = MagicMock()
+        mock_result.state = 'STARTED'
+        mock_result.abort.return_value = True
+        mock_async_result.return_value = mock_result
+
+        # Create completed experiment with task_id
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment with Task',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED,
+            task_id='active-task-id'
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Delete the experiment
+        url = f'/differential-expression/{experiment.pk}/delete'
+        response = self.client.delete(url)
+
+        # Assert success
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertTrue(response.data['ok'])
+
+        # Assert AbortableAsyncResult was called
+        mock_async_result.assert_called_once_with('active-task-id')
+        mock_result.abort.assert_called_once()
+
+        # Assert experiment was deleted
+        self.assertFalse(
+            DifferentialExpressionExperiment.objects.filter(pk=experiment.pk).exists()
+        )
+
+
+class DifferentialExpressionListTestCase(TestCase):
+    """Tests for DifferentialExpressionList endpoint"""
+
+    def setUp(self):
+        """Test setup"""
+        # Create test user
+        self.user = User.objects.create_user(
+            username='testuser',
+            email='test@test.com',
+            password='testpass123'
+        )
+
+        # Create test files
+        self.mrna_file = create_user_file(
+            get_test_file_path('mrna_test.csv'),
+            'mRNA Test',
+            FileType.MRNA,
+            self.user
+        )
+        self.clinical_file = create_user_file(
+            get_test_file_path('clinical_test.csv'),
+            'Clinical Test',
+            FileType.CLINICAL,
+            self.user
+        )
+
+        # Create sources
+        self.mrna_source = create_differential_expression_source(self.mrna_file)
+        self.clinical_source = create_differential_expression_clinical_source(self.clinical_file)
+
+        # Create API client
+        self.client = APIClient()
+
+    def test_list_experiments_authenticated(self):
+        """Test listing experiments when authenticated"""
+        # Create some experiments
+        create_test_differential_expression_experiment(
+            name='Experiment 1',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+        create_test_differential_expression_experiment(
+            name='Experiment 2',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user,
+            state=DifferentialExpressionExperimentState.IN_PROCESS
+        )
+
+        # Authenticate
+        self.client.force_authenticate(user=self.user)
+
+        # Get list
+        response = self.client.get('/differential-expression/')
+
+        # Assert success
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertEqual(response.data['count'], 2)
+
+    def test_list_experiments_not_authenticated(self):
+        """Test that unauthenticated users cannot list experiments"""
+        # Don't authenticate
+        response = self.client.get('/differential-expression/')
+
+        # Assert unauthorized
+        self.assertEqual(response.status_code, status.HTTP_401_UNAUTHORIZED)
+
+
+class DifferentialExpressionDetailTestCase(TestCase):
+    """Tests for DifferentialExpressionDetail endpoint"""
+
+    def setUp(self):
+        """Test setup"""
+        # Create test users
+        self.owner = User.objects.create_user(
+            username='owner',
+            email='owner@test.com',
+            password='testpass123'
+        )
+        self.other_user = User.objects.create_user(
+            username='other',
+            email='other@test.com',
+            password='testpass123'
+        )
+
+        # Create test files
+        self.mrna_file = create_user_file(
+            get_test_file_path('mrna_test.csv'),
+            'mRNA Test',
+            FileType.MRNA,
+            self.owner
+        )
+        self.clinical_file = create_user_file(
+            get_test_file_path('clinical_test.csv'),
+            'Clinical Test',
+            FileType.CLINICAL,
+            self.owner
+        )
+
+        # Create sources
+        self.mrna_source = create_differential_expression_source(self.mrna_file)
+        self.clinical_source = create_differential_expression_clinical_source(self.clinical_file)
+
+        # Create API client
+        self.client = APIClient()
+
+    def test_get_experiment_detail_as_owner(self):
+        """Test getting experiment detail as owner"""
+        experiment = create_test_differential_expression_experiment(
+            name='Test Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Get detail
+        response = self.client.get(f'/differential-expression/{experiment.pk}/')
+
+        # Assert success
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertEqual(response.data['name'], 'Test Experiment')
+
+    def test_get_experiment_detail_not_owner_private(self):
+        """Test that non-owner cannot access private experiment"""
+        experiment = create_test_differential_expression_experiment(
+            name='Private Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+        experiment.is_public = False
+        experiment.save()
+
+        # Authenticate as other user
+        self.client.force_authenticate(user=self.other_user)
+
+        # Try to get detail
+        response = self.client.get(f'/differential-expression/{experiment.pk}/')
+
+        # Assert bad request (ValidationError returns 400)
+        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
+
+    def test_get_experiment_detail_public(self):
+        """Test that anyone can access public experiment"""
+        experiment = create_test_differential_expression_experiment(
+            name='Public Experiment',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+        experiment.is_public = True
+        experiment.save()
+
+        # Authenticate as other user
+        self.client.force_authenticate(user=self.other_user)
+
+        # Get detail
+        response = self.client.get(f'/differential-expression/{experiment.pk}/')
+
+        # Assert success
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertEqual(response.data['name'], 'Public Experiment')
+
+
+class DifferentialExpressionUpdateTestCase(TestCase):
+    """Tests for DifferentialExpressionUpdate endpoint"""
+
+    def setUp(self):
+        """Test setup"""
+        # Create test users
+        self.owner = User.objects.create_user(
+            username='owner',
+            email='owner@test.com',
+            password='testpass123'
+        )
+        self.other_user = User.objects.create_user(
+            username='other',
+            email='other@test.com',
+            password='testpass123'
+        )
+
+        # Create test files
+        self.mrna_file = create_user_file(
+            get_test_file_path('mrna_test.csv'),
+            'mRNA Test',
+            FileType.MRNA,
+            self.owner
+        )
+        self.clinical_file = create_user_file(
+            get_test_file_path('clinical_test.csv'),
+            'Clinical Test',
+            FileType.CLINICAL,
+            self.owner
+        )
+
+        # Create sources
+        self.mrna_source = create_differential_expression_source(self.mrna_file)
+        self.clinical_source = create_differential_expression_clinical_source(self.clinical_file)
+
+        # Create API client
+        self.client = APIClient()
+
+    def test_update_experiment_name_and_description_success(self):
+        """Test successfully updating both name and description"""
+        # Create experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Original Name',
+            description='Original Description',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Update the experiment
+        url = f'/differential-expression/{experiment.pk}/update'
+        data = {
+            'name': 'Updated Name',
+            'description': 'Updated Description'
+        }
+        response = self.client.patch(url, data, format='json')
+
+        # Assert response
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertTrue(response.data['ok'])
+        self.assertEqual(response.data['data']['name'], 'Updated Name')
+        self.assertEqual(response.data['data']['description'], 'Updated Description')
+
+        # Assert experiment was updated in database
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.name, 'Updated Name')
+        self.assertEqual(experiment.description, 'Updated Description')
+
+    def test_update_experiment_name_only_success(self):
+        """Test successfully updating only the name"""
+        # Create experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Original Name',
+            description='Original Description',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Update only the name
+        url = f'/differential-expression/{experiment.pk}/update'
+        data = {'name': 'New Name Only'}
+        response = self.client.patch(url, data, format='json')
+
+        # Assert response
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertTrue(response.data['ok'])
+        self.assertEqual(response.data['data']['name'], 'New Name Only')
+        self.assertEqual(response.data['data']['description'], 'Original Description')
+
+        # Assert experiment was updated in database
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.name, 'New Name Only')
+        self.assertEqual(experiment.description, 'Original Description')
+
+    def test_update_experiment_description_only_success(self):
+        """Test successfully updating only the description"""
+        # Create experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Original Name',
+            description='Original Description',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Update only the description
+        url = f'/differential-expression/{experiment.pk}/update'
+        data = {'description': 'New Description Only'}
+        response = self.client.patch(url, data, format='json')
+
+        # Assert response
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertTrue(response.data['ok'])
+        self.assertEqual(response.data['data']['name'], 'Original Name')
+        self.assertEqual(response.data['data']['description'], 'New Description Only')
+
+        # Assert experiment was updated in database
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.name, 'Original Name')
+        self.assertEqual(experiment.description, 'New Description Only')
+
+    def test_update_experiment_not_owner(self):
+        """Test that non-owner cannot update experiment"""
+        # Create experiment owned by owner
+        experiment = create_test_differential_expression_experiment(
+            name='Original Name',
+            description='Original Description',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Authenticate as other user
+        self.client.force_authenticate(user=self.other_user)
+
+        # Try to update the experiment
+        url = f'/differential-expression/{experiment.pk}/update'
+        data = {'name': 'Hacked Name'}
+        response = self.client.patch(url, data, format='json')
+
+        # Assert forbidden
+        self.assertEqual(response.status_code, status.HTTP_403_FORBIDDEN)
+        self.assertFalse(response.data['ok'])
+
+        # Assert experiment was not updated
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.name, 'Original Name')
+
+    def test_update_experiment_no_fields_provided(self):
+        """Test that update fails when no fields are provided"""
+        # Create experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Original Name',
+            description='Original Description',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Try to update with no fields
+        url = f'/differential-expression/{experiment.pk}/update'
+        data = {}
+        response = self.client.patch(url, data, format='json')
+
+        # Assert bad request
+        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
+        self.assertFalse(response.data['ok'])
+        self.assertIn('at least one field', response.data['detail'].lower())
+
+        # Assert experiment was not updated
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.name, 'Original Name')
+        self.assertEqual(experiment.description, 'Original Description')
+
+    def test_update_experiment_not_authenticated(self):
+        """Test that unauthenticated user cannot update experiment"""
+        # Create experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Original Name',
+            description='Original Description',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Don't authenticate
+
+        # Try to update the experiment
+        url = f'/differential-expression/{experiment.pk}/update'
+        data = {'name': 'Hacked Name'}
+        response = self.client.patch(url, data, format='json')
+
+        # Assert unauthorized
+        self.assertEqual(response.status_code, status.HTTP_401_UNAUTHORIZED)
+
+        # Assert experiment was not updated
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.name, 'Original Name')
+
+    def test_update_experiment_not_found(self):
+        """Test updating non-existent experiment returns 404"""
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Try to update non-existent experiment
+        url = '/differential-expression/99999/update'
+        data = {'name': 'New Name'}
+        response = self.client.patch(url, data, format='json')
+
+        # Assert not found
+        self.assertEqual(response.status_code, status.HTTP_404_NOT_FOUND)
+
+    def test_update_experiment_empty_name(self):
+        """Test that updating experiment with empty name fails"""
+        # Create experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Original Name',
+            description='Original Description',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Try to update with empty name
+        url = f'/differential-expression/{experiment.pk}/update'
+        data = {'name': ''}
+        response = self.client.patch(url, data, format='json')
+
+        # Assert bad request
+        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
+        self.assertFalse(response.data['ok'])
+        self.assertIn('cannot be empty', response.data['detail'].lower())
+
+        # Assert experiment was not updated
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.name, 'Original Name')
+
+    def test_update_experiment_empty_description(self):
+        """Test that updating experiment with empty description succeeds"""
+        # Create experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Original Name',
+            description='Original Description',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.COMPLETED
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Update with empty description (should be allowed)
+        url = f'/differential-expression/{experiment.pk}/update'
+        data = {'description': ''}
+        response = self.client.patch(url, data, format='json')
+
+        # Assert success (empty description is valid)
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertTrue(response.data['ok'])
+        self.assertEqual(response.data['data']['name'], 'Original Name')
+        self.assertEqual(response.data['data']['description'], '')
+
+        # Assert experiment was updated in database
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.name, 'Original Name')
+        self.assertEqual(experiment.description, '')
+
+    def test_update_running_experiment(self):
+        """Test that running experiment can be updated (only name/description, not execution)"""
+        # Create a running experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Running Experiment',
+            description='Running Description',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.owner,
+            state=DifferentialExpressionExperimentState.IN_PROCESS,
+            task_id='test-task-id'
+        )
+
+        # Authenticate as owner
+        self.client.force_authenticate(user=self.owner)
+
+        # Update the experiment
+        url = f'/differential-expression/{experiment.pk}/update'
+        data = {'name': 'Updated Name While Running'}
+        response = self.client.patch(url, data, format='json')
+
+        # Assert success (name/description can be updated even while running)
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertTrue(response.data['ok'])
+        self.assertEqual(response.data['data']['name'], 'Updated Name While Running')
+
+        # Assert experiment was updated in database but state is still IN_PROCESS
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.name, 'Updated Name While Running')
+        self.assertEqual(experiment.state, DifferentialExpressionExperimentState.IN_PROCESS)
diff --git a/src/differential_expression/tests/tests_files/clinical_test.csv b/src/differential_expression/tests/tests_files/clinical_test.csv
new file mode 100644
index 00000000..9103f936
--- /dev/null
+++ b/src/differential_expression/tests/tests_files/clinical_test.csv
@@ -0,0 +1,5 @@
+,SAMPLE_1,SAMPLE_2,SAMPLE_3,SAMPLE_4,SAMPLE_5
+AGE,25,30,35,40,45
+GENDER,M,F,M,F,M
+STATUS,NORMAL,TUMOR,NORMAL,TUMOR,NORMAL
+STAGE,1,2,1,3,1
diff --git a/src/differential_expression/tests/tests_files/mrna_test.csv b/src/differential_expression/tests/tests_files/mrna_test.csv
new file mode 100644
index 00000000..b3a6ffc5
--- /dev/null
+++ b/src/differential_expression/tests/tests_files/mrna_test.csv
@@ -0,0 +1,6 @@
+,SAMPLE_1,SAMPLE_2,SAMPLE_3,SAMPLE_4,SAMPLE_5
+GENE_1,5.2,6.1,5.8,7.2,6.5
+GENE_2,3.1,3.5,3.2,4.1,3.8
+GENE_3,8.5,9.2,8.8,10.1,9.5
+GENE_4,2.3,2.8,2.5,3.2,2.9
+GENE_5,6.7,7.3,6.9,8.1,7.5
diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index 7f01e392..b172c8fa 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -7,6 +7,8 @@
     path('<int:pk>/results/', views.DifferentialExpressionResults.as_view()),
     path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
     path('stop-experiment', views.DifferentialExpressionStop.as_view(), name='differential_expression_stop'),
+    path('<int:pk>/update', views.DifferentialExpressionUpdate.as_view(), name='differential_expression_update'),
+    path('<int:pk>/delete', views.DifferentialExpressionDelete.as_view(), name='differential_expression_delete'),
     path('get-common-samples-differential-experiment', views.GetCommonSamplesDifferentialExperiment.as_view(), name='get_common_samples_differential_experiment'),
     path('get-common-samples-one-front-differential-experiment', views.GetCommonSamplesDifferentialOneFrontExperiment.as_view(), name='get_common_samples_one_front_differential_experiment'),
     path('switch-institution-public-view', views.ToggleDiffExperimentPublicView.as_view(), name='switch-diff-experiment-public-view'),
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 259df75d..90e9500b 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -5,7 +5,7 @@
 from django.db import transaction
 from django.db.models import Q
 from django_filters.rest_framework import DjangoFilterBackend
-from rest_framework import filters, generics, permissions
+from rest_framework import filters, generics, permissions, status
 from rest_framework.exceptions import ValidationError
 from rest_framework.generics import get_object_or_404
 from rest_framework.request import Request
@@ -505,6 +505,121 @@ def post(self, request):
             {"id": experiment.id, "is_public": experiment.is_public}
         )
 
+class DifferentialExpressionUpdate(APIView):
+    """
+    Endpoint to update name and description of a differential expression experiment.
+    Only the owner can update the experiment.
+    """
+    permission_classes = [permissions.IsAuthenticated]
+
+    @staticmethod
+    def patch(request: Request, pk: int):
+        """
+        Update name and/or description of a differential expression experiment.
+        """
+        experiment = get_object_or_404(DifferentialExpressionExperiment, pk=pk)
+
+        # Only the owner can update the experiment
+        if experiment.user.id != request.user.id:
+            return Response(
+                {'ok': False, 'detail': 'You do not have permission to update this experiment.'},
+                status=403
+            )
+
+        # Get the data from request
+        data = request.data
+        name = data.get('name')
+        description = data.get('description')
+
+        # Validate that at least one field is provided
+        if name is None and description is None:
+            return Response(
+                {'ok': False, 'detail': 'At least one field (name or description) must be provided.'},
+                status=400
+            )
+
+        # Validate that name is not empty if provided
+        if name is not None and not name:
+            return Response(
+                {'ok': False, 'detail': 'Experiment name cannot be empty.'},
+                status=400
+            )
+
+        # Update fields if provided
+        fields_to_update = []
+        if name is not None:
+            experiment.name = name
+            fields_to_update.append('name')
+        if description is not None:
+            experiment.description = description
+            fields_to_update.append('description')
+
+        # Save the experiment
+        experiment.save(update_fields=fields_to_update)
+
+        return Response({
+            'ok': True,
+            'data': {
+                'id': experiment.id,
+                'name': experiment.name,
+                'description': experiment.description
+            }
+        })
+
+
+class DifferentialExpressionDelete(APIView):
+    """
+    Endpoint to delete a differential expression experiment.
+    Only the owner can delete the experiment.
+    The experiment must not be running (must be completed, stopped, or in an error state).
+    """
+    permission_classes = [permissions.IsAuthenticated]
+
+    @staticmethod
+    def delete(request: Request, pk: int):
+        """
+        Delete a differential expression experiment.
+        """
+        experiment = get_object_or_404(DifferentialExpressionExperiment, pk=pk)
+
+        # Only the owner can delete the experiment
+        if experiment.user.id != request.user.id:
+            return Response(
+                {'ok': False, 'detail': 'You do not have permission to delete this experiment.'},
+                status=403
+            )
+
+        # Check if the experiment is currently running
+        running_states = [
+            DifferentialExpressionExperimentState.IN_PROCESS,
+            DifferentialExpressionExperimentState.WAITING_FOR_QUEUE,
+            DifferentialExpressionExperimentState.STOPPING,
+        ]
+
+        if experiment.state in running_states:
+            return Response(
+                {
+                    'ok': False,
+                    'detail': f'Cannot delete experiment while it is running. Current state: {experiment.get_state_display()}. Please stop the experiment first.'
+                },
+                status=400
+            )
+
+        # If the experiment has a task_id and is somehow still active, abort it
+        if experiment.task_id:
+            try:
+                async_res = AbortableAsyncResult(experiment.task_id)
+                if async_res.state in ['PENDING', 'STARTED', 'RETRY']:
+                    async_res.abort()
+            except Exception:
+                # If we can't abort, continue with deletion anyway since state shows it's not running
+                pass
+
+        # Delete the experiment (cascade will delete related objects)
+        experiment.delete()
+
+        return Response({'ok': True})
+
 
 def get_samples_list(
         id_source: int,

From fe6d38c89694db53e734c4bdbb48fa2db038d488 Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Tue, 14 Oct 2025 21:41:13 -0300
Subject: [PATCH 21/47] diferential expression page

---
 src/datasets_synchronization/views.py         |  9 ++-
 src/differential_expression/serializers.py    |  4 +-
 src/differential_expression/urls.py           |  6 +-
 src/differential_expression/views.py          |  2 +
 .../src/components/common/EditIcon.tsx        | 29 +++++++
 .../DifferentialExpressionForm.tsx            | 72 +++++++++++++++--
 ...entialExpressionInputClinicalAttribute.tsx |  3 +-
 .../DifferentialExpressionPanel.tsx           | 77 ++++++++++++++-----
 .../differential-expression/types.ts          |  9 ---
 .../AllExperimentsView.tsx                    |  8 +-
 .../EditExperimentIcon.tsx                    | 29 -------
 .../frontend/src/utils/django_interfaces.ts   |  3 +-
 .../frontend/differential-expression.html     |  3 +
 13 files changed, 181 insertions(+), 73 deletions(-)
 create mode 100644 src/frontend/static/frontend/src/components/common/EditIcon.tsx
 delete mode 100644 src/frontend/static/frontend/src/components/pipeline/all-experiments-view/EditExperimentIcon.tsx

diff --git a/src/datasets_synchronization/views.py b/src/datasets_synchronization/views.py
index 8650bcc7..2836376a 100644
--- a/src/datasets_synchronization/views.py
+++ b/src/datasets_synchronization/views.py
@@ -16,6 +16,8 @@
 from user_files.models_choices import FileType
 from .serializers import CGDSStudySerializer
 from django.shortcuts import render, get_object_or_404
+from api_service.utils import get_cgds_dataset
+from user_files.models_choices import FileType
 
 
 @login_required
@@ -223,5 +225,8 @@ class CGDSDatasetClinicalAttributes(APIView):
     @staticmethod
     def get(request, pk: int):
         """Gets the clinical attributes of a CGDSDataset."""
-        cgds_dataset: CGDSDataset = get_object_or_404(CGDSDataset, pk=pk)
-        return Response(cgds_dataset.get_column_names())
+        cgds_study = CGDSStudy.objects.get(pk=pk)
+        # Gets the corresponding Study's Dataset
+        cgds_dataset = get_cgds_dataset(cgds_study, FileType.CLINICAL)
+        list_of_samples = cgds_dataset.get_column_names()
+        return Response(list_of_samples)
diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index bcddccc4..d7d2d8fc 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -53,6 +53,7 @@ class DifferentialExpressionExperimentListSerializer(serializers.ModelSerializer
     # Sources - using standard API serializers compatible with frontend interfaces
     clinical_source = ExperimentClinicalSourceSerializer(read_only=True)
     mrna_source = ExperimentSourceSerializer(read_only=True)
+    user = UserSimpleSerializer(read_only=True)
 
     # State information
     state_display = serializers.CharField(source='get_state_display', read_only=True)
@@ -69,7 +70,8 @@ class Meta:
             'state_display',   # Human-readable state
             'clinical_source', # Clinical data source (ExperimentClinicalSourceSerializer)
             'mrna_source',     # mRNA data source (ExperimentSourceSerializer)
-            'is_public'        # Public visibility flag
+            'is_public',        # Public visibility flag
+            'tool'
         ]
         read_only_fields = [
             'id', 'created_at', 'state', 'state_display'
diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index b172c8fa..bbb9bc25 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -7,8 +7,10 @@
     path('<int:pk>/results/', views.DifferentialExpressionResults.as_view()),
     path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
     path('stop-experiment', views.DifferentialExpressionStop.as_view(), name='differential_expression_stop'),
-    path('<int:pk>/update', views.DifferentialExpressionUpdate.as_view(), name='differential_expression_update'),
-    path('<int:pk>/delete', views.DifferentialExpressionDelete.as_view(), name='differential_expression_delete'),
+    path('update', views.DifferentialExpressionUpdate.as_view(), name='differential_expression_update'),
+    path('update/<int:pk>/', views.DifferentialExpressionUpdate.as_view()),
+    path('delete', views.DifferentialExpressionDelete.as_view(), name='differential_expression_delete'),
+    path('delete/<int:pk>/', views.DifferentialExpressionDelete.as_view()),
     path('get-common-samples-differential-experiment', views.GetCommonSamplesDifferentialExperiment.as_view(), name='get_common_samples_differential_experiment'),
     path('get-common-samples-one-front-differential-experiment', views.GetCommonSamplesDifferentialOneFrontExperiment.as_view(), name='get_common_samples_one_front_differential_experiment'),
     path('switch-institution-public-view', views.ToggleDiffExperimentPublicView.as_view(), name='switch-diff-experiment-public-view'),
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 90e9500b..cd8ad675 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -156,6 +156,8 @@ def get_queryset(self):
     permission_classes = [permissions.IsAuthenticated]
     pagination_class = StandardResultsSetPagination
     filter_backends = [filters.OrderingFilter, filters.SearchFilter, DjangoFilterBackend]
+    search_fields = ['name', 'description']
+    filterset_fields = ['tool', ]
 
 
 class DifferentialExpressionSubmit(APIView):
diff --git a/src/frontend/static/frontend/src/components/common/EditIcon.tsx b/src/frontend/static/frontend/src/components/common/EditIcon.tsx
new file mode 100644
index 00000000..e4449128
--- /dev/null
+++ b/src/frontend/static/frontend/src/components/common/EditIcon.tsx
@@ -0,0 +1,29 @@
+import React, { useContext } from 'react'
+import { Icon } from 'semantic-ui-react'
+import { CurrentUserContext } from '../Base'
+import { Nullable } from '../../utils/interfaces'
+
+interface Props {
+    editExperiment: () => void,
+    ownerId: Nullable<number>,
+    disabled: boolean
+}
+
+export const EditIcon = (props: Props) => {
+    const currentUser = useContext(CurrentUserContext)
+
+    if (props.ownerId !== currentUser?.id) {
+        return <></>
+    }
+
+    return (
+        <Icon
+            name='pencil'
+            className='clickable margin-left-5'
+            color='yellow'
+            title='Edit'
+            onClick={props.editExperiment}
+            disabled={props.disabled}
+        />
+    )
+}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
index 7037d8f6..d7c6312c 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
@@ -1,4 +1,4 @@
-import React, { useRef, useState } from 'react'
+import React, { useEffect, useRef, useState } from 'react'
 import { Button, Form, Header, Icon, Label, PopupContentProps, Segment, SemanticShorthandItem } from 'semantic-ui-react'
 import { SourceForm } from '../pipeline/SourceForm'
 import { SingleRangeSlider } from 'neo-react-semantic-ui-range'
@@ -10,6 +10,7 @@ import ky from 'ky'
 import { MAX_FILE_SIZE_IN_MB_WARN } from '../../utils/constants'
 import { intersection, isEqual } from 'lodash'
 import { DifferentialExpressionInputClinicalAttribute } from './DifferentialExpressionInputClinicalAttribute'
+import { DifferentialExpressionAnalysis } from './types'
 
 // Define the possible field names for number of samples
 type NumberOfSamplesFields = 'numberOfSamplesMRNA' | 'numberOfSamplesClinical'
@@ -19,6 +20,7 @@ declare const urlGetCommonSamplesDiferentialExperiment: string
 declare const urlGetCommonSamplesOneFrontDiferentialExperiment: string
 declare const urlGetClinicalAttributes: string
 declare const urlCGDSDatasetClinicalAttributes: string
+declare const urlUpdateExperiment: string
 
 /** Available types of Sources for a DifferentialExpressionForm. */
 type SourceStateDifferentialExpression = 'clinicalSource' | 'mRNASource'
@@ -70,6 +72,8 @@ const cleanForm: IDifferentialExpressionForm = {
 }
 interface DifferentialExpressionFormProps {
     updateAlert: (type: CustomAlertTypes, msg: string) => void,
+    experimentToEdit: Nullable<DifferentialExpressionAnalysis>
+    handleCleanExperimentToEdit: () => void;
 }
 
 export const DifferentialExpressionForm = (props: DifferentialExpressionFormProps) => {
@@ -236,12 +240,47 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
             : num.toExponential()
     }
 
+    /**
+     * Handles the submit when is editting an experiment
+     * It sends only the fields that can be edited: name and description
+     */
+    const handleEditSubmit = () => {
+        setForm(prevState => ({
+            ...prevState,
+            isLoading: true
+        }))
+        const myHeaders = getDjangoHeader()
+
+        const body = {
+            name: form.differentialExpressionName,
+            description: form.differentialExpressionDescription
+        }
+
+        ky.patch(urlUpdateExperiment + `/${props.experimentToEdit?.id}/`, { headers: myHeaders, json: body }).then((response) => {
+            response.json().then(() => {
+                props.updateAlert(CustomAlertTypes.SUCCESS, 'Differential Expression experiment updated successfully!')
+                setForm(cleanForm)
+            }).catch((err) => {
+                console.error('Error parsing JSON ->', err)
+            })
+        }).catch((err) => {
+            console.error('Error to update experiment ->', err)
+            props.updateAlert(CustomAlertTypes.ERROR, 'Error to update Differential Expression experiment!')
+        }).finally(() => {
+            setForm(prevState => ({
+                ...prevState,
+                isLoading: false
+            }))
+        })
+    }
+
     const handleSubmit = () => {
         setForm(prevState => ({
             ...prevState,
             isLoading: true
         }))
         const myHeaders = getDjangoHeader()
+
         const body = {
             name: form.differentialExpressionName,
             description: form.differentialExpressionDescription,
@@ -259,6 +298,7 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
         ky.post(urlDifferentialExpressionSubmit, { headers: myHeaders, json: body }).then((response) => {
             response.json().then(() => {
                 props.updateAlert(CustomAlertTypes.SUCCESS, 'Differential Expression experiment created successfully!')
+                setForm(cleanForm)
             }).catch((err) => {
                 console.error('Error parsing JSON ->', err)
             })
@@ -531,7 +571,22 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
             form.differentialExpressionDescription.trim() === '' ||
             isEqual(form.mRNASource, () => getDefaultSource()) ||
             isEqual(form.clinicalSource, () => getDefaultSource())
-    )
+    ) && !(form.isEditing && form.differentialExpressionName.trim().length !== 0 && form.differentialExpressionDescription.trim().length !== 0)
+
+    /**
+     * Use effect to handle when is editting
+     */
+    useEffect(() => {
+        if (props.experimentToEdit) {
+            setForm(prevState => ({
+                ...prevState,
+                ...cleanForm,
+                isEditing: true,
+                differentialExpressionName: props.experimentToEdit?.name as string,
+                differentialExpressionDescription: props.experimentToEdit?.description as string
+            }))
+        }
+    }, [props.experimentToEdit])
 
     return (
         <Segment className='diff--side--bar--container table-bordered'>
@@ -617,6 +672,7 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                         optionsClinicalAttributes={form.optionsClinicalAttributes}
                         clinicalAttribute={form.clinicalAttribute}
                         onChange={(value: string) => handleChangeForm(value, 'clinicalAttribute')}
+                        isEditing={form.isEditing}
                     />
                 </Form.Field>
                 {/* Coefficient threshold slider */}{/* Minimum Standard Deviation for Genes */}
@@ -635,6 +691,7 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                         onChange={(value) => handleChangeForm(value, 'thresholdPercentile')}
                         className='diff--side--bar--slider'
                         color='blue'
+                        disabled={form.isEditing}
                     />
 
                     <Label color='blue' className='pull-left'>0</Label>
@@ -655,6 +712,7 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                         onChange={(value) => handleChangeForm(value, 'thresholdStd')}
                         className='diff--side--bar--slider'
                         color='blue'
+                        disabled={form.isEditing}
                     />
 
                     <Label color='blue' className='pull-left'>1e-4</Label>
@@ -675,6 +733,7 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                         onChange={(value) => handleChangeForm(value, 'top')}
                         className='diff--side--bar--slider'
                         color='blue'
+                        disabled={form.isEditing}
                     />
 
                     <Label color='blue' className='pull-left'>10</Label>
@@ -687,7 +746,7 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                     primary
                     className='margin-top-10'
                     disabled={submitDisabled || form.isLoading}
-                    onClick={handleSubmit}
+                    onClick={form.isEditing ? handleEditSubmit : handleSubmit}
                     color='green'
                     loading={form.isLoading}
                 >
@@ -698,9 +757,12 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                 className='margin-top-5'
                 fluid
                 primary
-                disabled={isEqual(form, cleanForm) || form.isLoading}
+                disabled={(isEqual(form, cleanForm)) || form.isLoading}
                 color='red'
-                onClick={() => setForm(cleanForm)}
+                onClick={() => {
+                    setForm(cleanForm)
+                    props.handleCleanExperimentToEdit()
+                }}
             >
                 {form.isEditing ? 'Cancel edit' : 'Reset form'}
             </Button>
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
index 3de92db1..7349dfeb 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
@@ -6,6 +6,7 @@ interface DifferentialExpressionInputClinicalAttributeProps {
     optionsClinicalAttributes: string[],
     clinicalAttribute: string,
     onChange: (value: string) => void,
+    isEditing: boolean,
 }
 
 export const DifferentialExpressionInputClinicalAttribute = (props: DifferentialExpressionInputClinicalAttributeProps) => {
@@ -24,7 +25,7 @@ export const DifferentialExpressionInputClinicalAttribute = (props: Differential
                 value={props.clinicalAttribute}
                 onChange={(_, { value }) => { props.onChange(value as string) }}
                 placeholder='Clinical attribute to group by'
-                disabled={false}
+                disabled={props.isEditing}
             />
         </>
     )
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index 7e50c6c8..5695b735 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -5,7 +5,7 @@ import { Confirm, DropdownItemProps, Grid, Icon, Table, TableCell } from 'semant
 import { PaginatedTable, PaginationCustomFilter } from '../common/PaginatedTable'
 import { TableCellWithTitle } from '../common/TableCellWithTitle'
 import { Alert } from '../common/Alert'
-import { ConfirmModal, CustomAlert, CustomAlertTypes, GenesColors } from '../../utils/interfaces'
+import { ConfirmModal, CustomAlert, CustomAlertTypes, GenesColors, Nullable } from '../../utils/interfaces'
 import { DifferentialExpressionAnalysis, DifferentialExpressionAnalysisExperimentState } from './types'
 import { formatDateLocale, getDefaultAlertProps, getDefaultConfirmModal, getDjangoHeader, getExperimentStateObj } from '../../utils/util_functions'
 import { SourcePopup } from '../pipeline/all-experiments-view/SourcePopup'
@@ -14,23 +14,34 @@ import { DeleteButton } from '../common/DeleteButton'
 import { SwitchPublicButton } from '../common/SwitchPublicButton'
 import { StopExperimentButton } from '../pipeline/all-experiments-view/StopExperimentButton'
 import ky from 'ky'
+import { EditIcon } from '../common/EditIcon'
 
 declare const urlDifferentialExpressionList:string
 declare const urlDifferentialExpressionStop:string
+declare const urlDeleteExperiment: string
 
 interface DiferentialExpressionPanelState {
     alert: CustomAlert
     modal: ConfirmModal
     stoppingExperiment: boolean
+    experimentToEdit: Nullable<DifferentialExpressionAnalysis>
 }
 
 export const DiferentialExpressionPanel = () => {
     const [state, setState] = useState<DiferentialExpressionPanelState>({
         alert: getDefaultAlertProps(),
         modal: getDefaultConfirmModal(),
-        stoppingExperiment: false
+        stoppingExperiment: false,
+        experimentToEdit: null
     })
 
+    const handleEdit = (differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
+        setState(prevState => ({
+            ...prevState,
+            experimentToEdit: differentialExpressionAnalysis
+        }))
+    }
+
     /**
      * Reset the confirm modal, to be used again
      */
@@ -61,18 +72,22 @@ export const DiferentialExpressionPanel = () => {
      * @returns Default object for table's Filters
      */
     const getDefaultFilters = (): PaginationCustomFilter[] => {
-        const tagOptions: DropdownItemProps[] = [{ id: 1, name: 'asd' }].map((tag) => {
+        const methodsOptions: DropdownItemProps[] = [{ id: 1, name: 'Lima' }, { id: 2, name: 'Deseq2' }].map((tag) => {
             const id = tag.id as number
             return { key: id, value: id, text: tag.name }
         })
 
-        tagOptions.unshift({ key: 'no_tag', text: 'No tag' })
+        methodsOptions.unshift({ key: 'no_method', text: 'No method' })
 
         return [
-            { label: 'Tag', keyForServer: 'tag', defaultValue: '', placeholder: 'Select an existing Tag', options: tagOptions, width: 3 }
+            { label: 'Method', keyForServer: 'method', defaultValue: '', placeholder: 'Select an existing method', options: methodsOptions, width: 3 }
         ]
     }
 
+    /**
+     * Stop experiment
+     * @param experimentId experiment to stop
+     */
     const confirmExperimentStop = (experimentId: number) => {
         const myHeaders = getDjangoHeader()
 
@@ -94,9 +109,25 @@ export const DiferentialExpressionPanel = () => {
         })
     }
 
+    /**
+     * Delete experiment
+     * @param differentialExpressionAnalysis experiment to delete
+     */
     const confirmExperimentDeletion = (differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
-        // To implement
-        console.log(differentialExpressionAnalysis)
+        const myHeaders = getDjangoHeader()
+
+        ky.delete(urlDeleteExperiment + `/${differentialExpressionAnalysis.id}/`, {
+            headers: myHeaders,
+        }).then((response) => {
+            if (response.ok) {
+                updateAlert(CustomAlertTypes.SUCCESS, 'Differential Expression experiment deleted successfully!')
+            } else {
+                updateAlert(CustomAlertTypes.ERROR, 'Error deleting Differential Expression experiment!')
+            }
+        }).catch((err) => {
+            updateAlert(CustomAlertTypes.ERROR, 'Error deleting Differential Expression experiment!')
+            console.error('Error deleting FSExperiment ->', err)
+        })
     }
 
     /**
@@ -129,13 +160,22 @@ export const DiferentialExpressionPanel = () => {
         }))
     }
 
+    const handleCleanExperimentToEdit = () => {
+        setState(prevState => ({
+            ...prevState,
+            experimentToEdit: null
+        }))
+    }
+
     return (
         <Base activeItem='differential-expression' wrapperClass='wrapper'>
             <Grid columns={2} padded stackable divided className='biomarkers--modal--container'>
                 <Grid.Column width={4} textAlign='center'>
-
-                    <DifferentialExpressionForm updateAlert={updateAlert} />
-
+                    <DifferentialExpressionForm
+                        updateAlert={updateAlert}
+                        experimentToEdit={state.experimentToEdit}
+                        handleCleanExperimentToEdit={handleCleanExperimentToEdit}
+                    />
                 </Grid.Column>
                 <Grid.Column width={12}>
                     <PaginatedTable<DifferentialExpressionAnalysis>
@@ -149,7 +189,7 @@ export const DiferentialExpressionPanel = () => {
                             { name: 'Public', width: 1 },
                             { name: 'Actions', width: 2 }
                         ]}
-                        defaultSortProp={{ sortField: 'upload_date', sortOrderAscendant: false }}
+                        defaultSortProp={{ sortField: 'created_at', sortOrderAscendant: false }}
                         customFilters={getDefaultFilters()}
                         showSearchInput
                         customElements={[
@@ -163,12 +203,11 @@ export const DiferentialExpressionPanel = () => {
                                 </Button>
                             </Form.Field> */
                         ]}
-                        searchLabel='Name'
-                        searchPlaceholder='Search by name'
+                        searchLabel='Name/Description'
+                        searchPlaceholder='Search by name/description'
                         urlToRetrieveData={urlDifferentialExpressionList}
                         updateWSKey='update_differential_expression_experiments'
                         mapFunction={(differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
-                            console.log(differentialExpressionAnalysis)
                             const isInProcess = differentialExpressionAnalysis.state === DifferentialExpressionAnalysisExperimentState.IN_PROCESS ||
                             differentialExpressionAnalysis.state === DifferentialExpressionAnalysisExperimentState.WAITING_FOR_QUEUE
 
@@ -234,11 +273,11 @@ export const DiferentialExpressionPanel = () => {
                                         {/* See results button */}
 
                                         {/* Edit button */}
-                                        {/* <EditExperimentIcon
-                                            editExperiment={this.props.editExperiment}
-                                            experiment={experiment}
-                                            ownerId={experiment.user.id}
-                                        /> */}
+                                        <EditIcon
+                                            editExperiment={() => handleEdit(differentialExpressionAnalysis)}
+                                            ownerId={differentialExpressionAnalysis.user.id}
+                                            disabled={differentialExpressionAnalysis.state === DifferentialExpressionAnalysisExperimentState.COMPLETED}
+                                        />
 
                                         <PopupIcons
                                             content={(
diff --git a/src/frontend/static/frontend/src/components/differential-expression/types.ts b/src/frontend/static/frontend/src/components/differential-expression/types.ts
index 71fd1050..30f3ce9f 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/types.ts
+++ b/src/frontend/static/frontend/src/components/differential-expression/types.ts
@@ -21,17 +21,8 @@ export interface DifferentialExpressionAnalysis {
     user: DjangoUser;
     clinical_source: DjangoExperimentSource;
     mrna_source: DjangoExperimentSource;
-    clinical_attribute: string;
-    threshold_percentile: number;
-    threshold: number;
-    top: number;
     state: DifferentialExpressionAnalysisExperimentState;
     state_display: string;
-    execution_time: number;
     created_at: string;
-    updated_at: string;
     is_public: boolean;
-    has_results: boolean;
-    results_count: number;
-    significant_genes_count: number;
 }
diff --git a/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/AllExperimentsView.tsx b/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/AllExperimentsView.tsx
index affc4616..8939a95a 100644
--- a/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/AllExperimentsView.tsx
+++ b/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/AllExperimentsView.tsx
@@ -13,7 +13,7 @@ import { DeleteButton } from '../../common/DeleteButton'
 import { SharedInstitutions, SharedInstitutionsProps } from './SharedInstitutions'
 import { SwitchPublicButton } from '../../common/SwitchPublicButton'
 import { SharedUsers, SharedUsersProps } from './SharedUsers'
-import { EditExperimentIcon } from './EditExperimentIcon'
+import { EditIcon } from '../../common/EditIcon'
 import { PopupIcons } from '../../common/PopupIcons'
 
 declare const urlUserExperiments: string
@@ -316,10 +316,10 @@ export class AllExperimentsView extends React.Component<AllExperimentsViewProps,
                                     <SeeResultButton experiment={experiment} seeResult={this.props.seeResult} />
 
                                     {/* Edit button */}
-                                    <EditExperimentIcon
-                                        editExperiment={this.props.editExperiment}
-                                        experiment={experiment}
+                                    <EditIcon
+                                        editExperiment={() => this.props.editExperiment(experiment)}
                                         ownerId={experiment.user.id}
+                                        disabled={experiment.state !== ExperimentState.COMPLETED}
                                     />
 
                                     <PopupIcons
diff --git a/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/EditExperimentIcon.tsx b/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/EditExperimentIcon.tsx
deleted file mode 100644
index def8cdf4..00000000
--- a/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/EditExperimentIcon.tsx
+++ /dev/null
@@ -1,29 +0,0 @@
-import React, { useContext } from 'react'
-import { Icon } from 'semantic-ui-react'
-import { DjangoExperiment, ExperimentState } from '../../../utils/django_interfaces'
-import { CurrentUserContext } from '../../Base'
-
-interface Props {
-    editExperiment: (experiment: DjangoExperiment) => void,
-    experiment: DjangoExperiment,
-    ownerId: number,
-}
-
-export const EditExperimentIcon = (props: Props) => {
-    const currentUser = useContext(CurrentUserContext)
-
-    if (props.ownerId !== currentUser?.id) {
-        return <></>
-    }
-
-    return (
-        <Icon
-            name='pencil'
-            className='clickable margin-left-5'
-            color='yellow'
-            title='Edit'
-            onClick={() => props.editExperiment(props.experiment)}
-            disabled={props.experiment.state !== ExperimentState.COMPLETED}
-        />
-    )
-}
diff --git a/src/frontend/static/frontend/src/utils/django_interfaces.ts b/src/frontend/static/frontend/src/utils/django_interfaces.ts
index 777b4ae5..efcf887d 100644
--- a/src/frontend/static/frontend/src/utils/django_interfaces.ts
+++ b/src/frontend/static/frontend/src/utils/django_interfaces.ts
@@ -241,7 +241,7 @@ interface DjangoUserFile extends DjangoSimpleUserFile {
 }
 
 /**
- * Django Model api_service.ExperimentSource
+ * Django Model api_service.ExperimentSource todo agregar opcional update_differential_expression_experiments
  */
 interface DjangoExperimentSource {
     id?: number,
@@ -249,6 +249,7 @@ interface DjangoExperimentSource {
     cgds_dataset: SourceSimpleCGDSDataset,
     number_of_rows: number,
     number_of_samples: number
+    extra_cgds_dataset?: SourceSimpleCGDSDataset;
 }
 
 /**
diff --git a/src/frontend/templates/frontend/differential-expression.html b/src/frontend/templates/frontend/differential-expression.html
index b7f43f19..e0e493d3 100644
--- a/src/frontend/templates/frontend/differential-expression.html
+++ b/src/frontend/templates/frontend/differential-expression.html
@@ -23,6 +23,9 @@
             const urlPostSwitchPublicView = "{% url 'switch-diff-experiment-public-view' %}"
             const urlDifferentialExpressionStop = "{% url 'differential_expression_stop' %}"
             const urlCGDSDatasetClinicalAttributes = "{% url 'cgds_dataset_clinical_attributes' %}"
+            const downloadFileURL = "{% url 'download_user_file' %}"
+            const urlDeleteExperiment = "{% url 'differential_expression_delete' %}"
+            const urlUpdateExperiment = "{% url 'differential_expression_update' %}"
         </script>
         {% render_bundle 'differentialExpression' 'js' %}
 {% endblock %}
\ No newline at end of file

From 9afc0a8f3f020c7d3019285c345edcb45742ad3a Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Fri, 24 Oct 2025 13:46:28 -0300
Subject: [PATCH 22/47] diffExpressionBase

---
 src/differential_expression/urls.py           |   4 +-
 .../static/frontend/package-lock.json         | 144 +++++++-----------
 .../DifferentialExpressionForm.tsx            |  19 ++-
 .../DifferentialExpressionModalResults.tsx    |  64 ++++++++
 .../DifferentialExpressionPanel.tsx           |  44 +++++-
 .../differential-expression/types.ts          |  13 +-
 .../src/css/differential-expression.css       |  10 ++
 .../frontend/src/utils/util_functions.ts      |  90 ++++++++++-
 .../frontend/differential-expression.html     |   1 +
 9 files changed, 280 insertions(+), 109 deletions(-)
 create mode 100644 src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx

diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index bbb9bc25..1c4cd008 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -3,8 +3,8 @@
 
 urlpatterns = [
     path('', views.DifferentialExpressionList.as_view(), name='differential_expression_list'),
-    path('<int:pk>/', views.DifferentialExpressionDetail.as_view()),
-    path('<int:pk>/results/', views.DifferentialExpressionResults.as_view()),
+    path('results/', views.DifferentialExpressionDetail.as_view(), name='differential_expression_results'),
+    path('results/<int:pk>/', views.DifferentialExpressionResults.as_view()),
     path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
     path('stop-experiment', views.DifferentialExpressionStop.as_view(), name='differential_expression_stop'),
     path('update', views.DifferentialExpressionUpdate.as_view(), name='differential_expression_update'),
diff --git a/src/frontend/static/frontend/package-lock.json b/src/frontend/static/frontend/package-lock.json
index 9e29f6d6..1b114777 100644
--- a/src/frontend/static/frontend/package-lock.json
+++ b/src/frontend/static/frontend/package-lock.json
@@ -126,6 +126,7 @@
       "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.28.0.tgz",
       "integrity": "sha512-UlLAnTPrFdNGoFtbSXwcGFQBtQZJCNjaN6hQNP3UPvuNXT1i82N26KL3dZeIpNalWywr9IuQuncaAfUaS1g6sQ==",
       "license": "MIT",
+      "peer": true,
       "dependencies": {
         "@ampproject/remapping": "^2.2.0",
         "@babel/code-frame": "^7.27.1",
@@ -2122,6 +2123,7 @@
       "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.27.1.tgz",
       "integrity": "sha512-1x3D2xEk2fRo3PAhwQwu5UubzgiVWSXTBfWpVd2Mx2AzRqJuDJCsgaDVZ7HB5iGzDW1Hl1sWN2mFyKjmR9uAog==",
       "license": "MIT",
+      "peer": true,
       "engines": {
         "node": ">=6.9.0"
       }
@@ -3880,6 +3882,7 @@
       "version": "2.11.8",
       "resolved": "https://registry.npmjs.org/@popperjs/core/-/core-2.11.8.tgz",
       "integrity": "sha512-P1st0aksCrn9sGZhp8GMYwBnQsbvAWsZAX44oXNNvLHGqAOcoVxmjZiohstwQ7SqKnbR47akdNi+uleWD8+g6A==",
+      "peer": true,
       "funding": {
         "type": "opencollective",
         "url": "https://opencollective.com/popperjs"
@@ -4198,6 +4201,7 @@
       "resolved": "https://registry.npmjs.org/@rspack/core/-/core-1.3.2.tgz",
       "integrity": "sha512-QbEn1SkNW3b89KTlSkp6OHdvw3DhpL6tSdDhsOlldw3LoRBy4fx80Z9W9lmg+g+8DjTAs1Z1ysElEFtAN69AZg==",
       "dev": true,
+      "peer": true,
       "dependencies": {
         "@module-federation/runtime-tools": "0.11.2",
         "@rspack/binding": "1.3.2",
@@ -4248,6 +4252,7 @@
       "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.17.1.tgz",
       "integrity": "sha512-B/gBuNg5SiMTrPkC+A2+cW0RszwxYmn6VYxB/inlBStS5nx6xHIt/ehKRhIMhqusl7a8LjQoZnjCs5vhwxOQ1g==",
       "dev": true,
+      "peer": true,
       "dependencies": {
         "fast-deep-equal": "^3.1.3",
         "fast-uri": "^3.0.1",
@@ -4884,7 +4889,6 @@
       "integrity": "sha512-JQ5TuMi45Owi4/BIMAJBoSQoOJu12oOk/gADqlcUL9JEdHB8vyjUSsxqeNXnmXHjYKMi2WcYtezGEEhqUI/E2g==",
       "dev": true,
       "optional": true,
-      "peer": true,
       "dependencies": {
         "tslib": "^2.8.0"
       }
@@ -4894,8 +4898,7 @@
       "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.8.1.tgz",
       "integrity": "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w==",
       "dev": true,
-      "optional": true,
-      "peer": true
+      "optional": true
     },
     "node_modules/@tootallnate/once": {
       "version": "1.1.2",
@@ -5256,7 +5259,6 @@
       "version": "3.7.7",
       "resolved": "https://registry.npmjs.org/@types/eslint-scope/-/eslint-scope-3.7.7.tgz",
       "integrity": "sha512-MzMFlSLBqNF2gcHWO0G1vP/YQyfvrxZ0bF+u7mzUdZ1/xK4A4sru+nraZz5i3iEIk1l1uyicaDVTB4QbbEkAYg==",
-      "peer": true,
       "dependencies": {
         "@types/eslint": "*",
         "@types/estree": "*"
@@ -5390,6 +5392,7 @@
       "version": "12.2.3",
       "resolved": "https://registry.npmjs.org/@types/markdown-it/-/markdown-it-12.2.3.tgz",
       "integrity": "sha512-GKMHFfv3458yYy+v/N8gjufHO6MSZKCOXpZc5GXIWWy8uldwfmPn98vp81gZ5f9SVw8YYBctgfJ22a2d7AOMeQ==",
+      "peer": true,
       "dependencies": {
         "@types/linkify-it": "*",
         "@types/mdurl": "*"
@@ -5471,6 +5474,7 @@
       "version": "18.3.20",
       "resolved": "https://registry.npmjs.org/@types/react/-/react-18.3.20.tgz",
       "integrity": "sha512-IPaCZN7PShZK/3t6Q87pfTkRm6oLTd4vztyoj+cbHUF1g3FfVb2tFIL79uCRKEfv16AhqDMBywP2VW3KIZUvcg==",
+      "peer": true,
       "dependencies": {
         "@types/prop-types": "*",
         "csstype": "^3.0.2"
@@ -5593,6 +5597,7 @@
       "version": "4.41.32",
       "resolved": "https://registry.npmjs.org/@types/webpack/-/webpack-4.41.32.tgz",
       "integrity": "sha512-cb+0ioil/7oz5//7tZUSwbrSAN/NWHrQylz5cW8G0dWTcF/g+/dSdMlKVZspBYuMAN1+WnwHrkxiRrLcwd0Heg==",
+      "peer": true,
       "dependencies": {
         "@types/node": "*",
         "@types/tapable": "^1",
@@ -5701,6 +5706,7 @@
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@@ -26605,14 +26607,12 @@
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-      "peer": true
+      "integrity": "sha512-NM8/P9n3XjXhIZn1lLhkFaACTOURQXjWhV4BA/RnOv8xvgqtqpAX9IO4mRQxSx1Rlo4tqzeqb0sOlruaOy3dug=="
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@@ -26631,7 +26631,6 @@
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@@ -26640,7 +26639,6 @@
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@@ -26655,7 +26653,6 @@
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@@ -26775,6 +26772,7 @@
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       "dev": true,
+      "peer": true,
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       },
@@ -27187,19 +27185,6 @@
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       }
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-    "node_modules/type-fest": {
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-      "optional": true,
-      "peer": true,
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-      }
-    },
     "node_modules/type-is": {
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@@ -27304,6 +27289,7 @@
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+      "peer": true,
       "bin": {
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         "tsserver": "bin/tsserver"
@@ -28404,6 +28390,7 @@
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+      "peer": true,
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         "ansi-html": "0.0.7",
         "bonjour": "^3.5.0",
@@ -29098,7 +29085,6 @@
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         "@webassemblyjs/helper-wasm-bytecode": "1.13.2"
@@ -29107,26 +29093,22 @@
     "node_modules/webpack/node_modules/@webassemblyjs/helper-api-error": {
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-      "peer": true
+      "integrity": "sha512-U56GMYxy4ZQCbDZd6JuvvNV/WFildOjsaWD3Tzzvmw/mas3cXzRJPMjP83JqEsgSbyrmaGjBfDtV7KDXV9UzFQ=="
     },
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       "version": "1.14.1",
       "resolved": "https://registry.npmjs.org/@webassemblyjs/helper-buffer/-/helper-buffer-1.14.1.tgz",
-      "integrity": "sha512-jyH7wtcHiKssDtFPRB+iQdxlDf96m0E39yb0k5uJVhFGleZFoNw1c4aeIcVUPPbXUVJ94wwnMOAqUHyzoEPVMA==",
-      "peer": true
+      "integrity": "sha512-jyH7wtcHiKssDtFPRB+iQdxlDf96m0E39yb0k5uJVhFGleZFoNw1c4aeIcVUPPbXUVJ94wwnMOAqUHyzoEPVMA=="
     },
     "node_modules/webpack/node_modules/@webassemblyjs/helper-wasm-bytecode": {
       "version": "1.13.2",
       "resolved": "https://registry.npmjs.org/@webassemblyjs/helper-wasm-bytecode/-/helper-wasm-bytecode-1.13.2.tgz",
-      "integrity": "sha512-3QbLKy93F0EAIXLh0ogEVR6rOubA9AoZ+WRYhNbFyuB70j3dRdwH9g+qXhLAO0kiYGlg3TxDV+I4rQTr/YNXkA==",
-      "peer": true
+      "integrity": "sha512-3QbLKy93F0EAIXLh0ogEVR6rOubA9AoZ+WRYhNbFyuB70j3dRdwH9g+qXhLAO0kiYGlg3TxDV+I4rQTr/YNXkA=="
     },
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       "resolved": "https://registry.npmjs.org/@webassemblyjs/helper-wasm-section/-/helper-wasm-section-1.14.1.tgz",
       "integrity": "sha512-ds5mXEqTJ6oxRoqjhWDU83OgzAYjwsCV8Lo/N+oRsNDmx/ZDpqalmrtgOMkHwxsG0iI//3BwWAErYRHtgn0dZw==",
-      "peer": true,
       "dependencies": {
         "@webassemblyjs/ast": "1.14.1",
         "@webassemblyjs/helper-buffer": "1.14.1",
@@ -29138,7 +29120,6 @@
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       "resolved": "https://registry.npmjs.org/@webassemblyjs/ieee754/-/ieee754-1.13.2.tgz",
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-      "peer": true,
       "dependencies": {
         "@xtuc/ieee754": "^1.2.0"
       }
@@ -29147,7 +29128,6 @@
       "version": "1.13.2",
       "resolved": "https://registry.npmjs.org/@webassemblyjs/leb128/-/leb128-1.13.2.tgz",
       "integrity": "sha512-Lde1oNoIdzVzdkNEAWZ1dZ5orIbff80YPdHx20mrHwHrVNNTjNr8E3xz9BdpcGqRQbAEa+fkrCb+fRFTl/6sQw==",
-      "peer": true,
       "dependencies": {
         "@xtuc/long": "4.2.2"
       }
@@ -29155,14 +29135,12 @@
     "node_modules/webpack/node_modules/@webassemblyjs/utf8": {
       "version": "1.13.2",
       "resolved": "https://registry.npmjs.org/@webassemblyjs/utf8/-/utf8-1.13.2.tgz",
-      "integrity": "sha512-3NQWGjKTASY1xV5m7Hr0iPeXD9+RDobLll3T9d2AO+g3my8xy5peVyjSag4I50mR1bBSN/Ct12lo+R9tJk0NZQ==",
-      "peer": true
+      "integrity": "sha512-3NQWGjKTASY1xV5m7Hr0iPeXD9+RDobLll3T9d2AO+g3my8xy5peVyjSag4I50mR1bBSN/Ct12lo+R9tJk0NZQ=="
     },
     "node_modules/webpack/node_modules/@webassemblyjs/wasm-edit": {
       "version": "1.14.1",
       "resolved": "https://registry.npmjs.org/@webassemblyjs/wasm-edit/-/wasm-edit-1.14.1.tgz",
       "integrity": "sha512-RNJUIQH/J8iA/1NzlE4N7KtyZNHi3w7at7hDjvRNm5rcUXa00z1vRz3glZoULfJ5mpvYhLybmVcwcjGrC1pRrQ==",
-      "peer": true,
       "dependencies": {
         "@webassemblyjs/ast": "1.14.1",
         "@webassemblyjs/helper-buffer": "1.14.1",
@@ -29178,7 +29156,6 @@
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       "resolved": "https://registry.npmjs.org/@webassemblyjs/wasm-gen/-/wasm-gen-1.14.1.tgz",
       "integrity": "sha512-AmomSIjP8ZbfGQhumkNvgC33AY7qtMCXnN6bL2u2Js4gVCg8fp735aEiMSBbDR7UQIj90n4wKAFUSEd0QN2Ukg==",
-      "peer": true,
       "dependencies": {
         "@webassemblyjs/ast": "1.14.1",
         "@webassemblyjs/helper-wasm-bytecode": "1.13.2",
@@ -29191,7 +29168,6 @@
       "version": "1.14.1",
       "resolved": "https://registry.npmjs.org/@webassemblyjs/wasm-opt/-/wasm-opt-1.14.1.tgz",
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-      "peer": true,
       "dependencies": {
         "@webassemblyjs/ast": "1.14.1",
         "@webassemblyjs/helper-buffer": "1.14.1",
@@ -29203,7 +29179,6 @@
       "version": "1.14.1",
       "resolved": "https://registry.npmjs.org/@webassemblyjs/wasm-parser/-/wasm-parser-1.14.1.tgz",
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-      "peer": true,
       "dependencies": {
         "@webassemblyjs/ast": "1.14.1",
         "@webassemblyjs/helper-api-error": "1.13.2",
@@ -29217,7 +29192,6 @@
       "version": "1.14.1",
       "resolved": "https://registry.npmjs.org/@webassemblyjs/wast-printer/-/wast-printer-1.14.1.tgz",
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-      "peer": true,
       "dependencies": {
         "@webassemblyjs/ast": "1.14.1",
         "@xtuc/long": "4.2.2"
@@ -29227,7 +29201,6 @@
       "version": "8.14.1",
       "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.14.1.tgz",
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-      "peer": true,
       "bin": {
         "acorn": "bin/acorn"
       },
@@ -29257,7 +29230,6 @@
       "resolved": "https://registry.npmjs.org/ajv-keywords/-/ajv-keywords-5.1.0.tgz",
       "integrity": "sha512-YCS/JNFAUyr5vAuhk1DWm1CBxRHW9LbJ2ozWeemrIqpbsqKjHVxYPyi5GC0rjZIT5JxJ3virVTS8wk4i/Z+krw==",
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "fast-deep-equal": "^3.1.3"
       },
@@ -29269,7 +29241,6 @@
       "version": "5.17.1",
       "resolved": "https://registry.npmjs.org/enhanced-resolve/-/enhanced-resolve-5.17.1.tgz",
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-      "peer": true,
       "dependencies": {
         "graceful-fs": "^4.2.4",
         "tapable": "^2.2.0"
@@ -29282,14 +29253,12 @@
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-1.0.0.tgz",
       "integrity": "sha512-NM8/P9n3XjXhIZn1lLhkFaACTOURQXjWhV4BA/RnOv8xvgqtqpAX9IO4mRQxSx1Rlo4tqzeqb0sOlruaOy3dug==",
-      "license": "MIT",
-      "peer": true
+      "license": "MIT"
     },
     "node_modules/webpack/node_modules/loader-runner": {
       "version": "4.3.0",
       "resolved": "https://registry.npmjs.org/loader-runner/-/loader-runner-4.3.0.tgz",
       "integrity": "sha512-3R/1M+yS3j5ou80Me59j7F9IMs4PXs3VqRrm0TU3AbKPxlmpoY1TNscJV/oGJXo8qCatFGTfDbY6W6ipGOYXfg==",
-      "peer": true,
       "engines": {
         "node": ">=6.11.5"
       }
@@ -29299,7 +29268,6 @@
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       "integrity": "sha512-Gn/JaSk/Mt9gYubxTtSn/QCV4em9mpAPiR1rqy/Ocu19u/G9J5WWdNoUT4SiV6mFC3y6cxyFcFwdzPM3FgxGAQ==",
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@types/json-schema": "^7.0.9",
         "ajv": "^8.9.0",
@@ -29318,7 +29286,6 @@
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-      "peer": true,
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         "node": ">=6"
       }
@@ -29327,7 +29294,6 @@
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-      "peer": true,
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         "glob-to-regexp": "^0.4.1",
         "graceful-fs": "^4.1.2"
@@ -29340,7 +29306,6 @@
       "version": "3.2.3",
       "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.2.3.tgz",
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-      "peer": true,
       "engines": {
         "node": ">=10.13.0"
       }
@@ -29962,6 +29927,7 @@
       "integrity": "sha512-gzUt/qt81nXsFGKIFcC3YnfEAx5NkunCfnDlvuBSSFS02bcXu4Lmea0AFIUwbLWxWPx3d9p8S5QoaujKcNQxcQ==",
       "dev": true,
       "license": "MIT",
+      "peer": true,
       "funding": {
         "url": "https://github.com/sponsors/colinhacks"
       }
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
index d7c6312c..e356ad87 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
@@ -423,10 +423,14 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                         console.error('Error parsing JSON ->', err)
                     })
                 }).catch((err) => {
-                    setForm(prevState => ({ ...prevState, gettingCommonSamples: false }))
                     console.error('Error getting user experiments', err)
                 })
-            }).catch(errorReadingFileInInput)
+            }).catch(errorReadingFileInInput).finally(() => {
+                setForm(prevState => ({
+                    ...prevState,
+                    gettingCommonSamples: false
+                }))
+            })
         }
     }
 
@@ -473,6 +477,11 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                 }
 
                 console.error('Error getting user experiments', err)
+            }).finally(() => {
+                setForm(prevState => ({
+                    ...prevState,
+                    gettingCommonSamples: false
+                }))
             })
         }
     }
@@ -688,7 +697,7 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                         defaultMinValue={0}
                         step={0.05}
                         value={form.thresholdPercentile}
-                        onChange={(value) => handleChangeForm(value, 'thresholdPercentile')}
+                        onChange={(value) => form.isEditing && handleChangeForm(value, 'thresholdPercentile')}
                         className='diff--side--bar--slider'
                         color='blue'
                         disabled={form.isEditing}
@@ -709,7 +718,7 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                         defaultMinValue={0.0001}
                         step={0.0001}
                         value={form.thresholdStd}
-                        onChange={(value) => handleChangeForm(value, 'thresholdStd')}
+                        onChange={(value) => form.isEditing && handleChangeForm(value, 'thresholdStd')}
                         className='diff--side--bar--slider'
                         color='blue'
                         disabled={form.isEditing}
@@ -730,7 +739,7 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
                         defaultMinValue={10}
                         step={10}
                         value={form.top}
-                        onChange={(value) => handleChangeForm(value, 'top')}
+                        onChange={(value) => form.isEditing && handleChangeForm(value, 'top')}
                         className='diff--side--bar--slider'
                         color='blue'
                         disabled={form.isEditing}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
new file mode 100644
index 00000000..1d3d842e
--- /dev/null
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
@@ -0,0 +1,64 @@
+import React from 'react'
+import { DifferentialExpressionAnalysis } from './types'
+import { Icon, Modal, Table, TableCell } from 'semantic-ui-react'
+import { TableCellWithTitle } from '../common/TableCellWithTitle'
+import { PaginatedTable } from '../common/PaginatedTable'
+
+declare const urlDifferentialExpressionExperimentResults: string
+
+interface DifferentialExpressionModalResultsProps {
+    isOpen: boolean
+    differentialExpressionAnalysis: DifferentialExpressionAnalysis | null
+    closeModal: () => void
+}
+
+export const DifferentialExpressionModalResults = (props: DifferentialExpressionModalResultsProps) => {
+    return (
+        <Modal
+            open={props.isOpen}
+            closeIcon={<Icon name='close' size='large' />}
+            closeOnEscape={false}
+            closeOnDimmerClick={false}
+            closeOnDocumentClick={false}
+            className='space-modal large-modal'
+            onClose={props.closeModal}
+        >
+            <PaginatedTable<DifferentialExpressionAnalysis>
+                headerTitle='Differential Expressions experiment result'
+                headers={[
+                    { name: 'Name', serverCodeToSort: 'name', width: 3 },
+                    { name: 'Description', serverCodeToSort: 'description', width: 4 },
+                ]}
+                defaultSortProp={{ sortField: 'created_at', sortOrderAscendant: false }}
+                customFilters={undefined}
+                showSearchInput
+                customElements={[
+                    /*  <Form.Field key={1} className='custom-table-field' title='Add new Biomarker'>
+                        <Button
+                            primary
+                            icon
+                            onClick={() => this.setState({ formBiomarker: this.getDefaultFormBiomarker(), openCreateEditBiomarkerModal: true })}
+                        >
+                            <Icon name='add' />
+                        </Button>
+                    </Form.Field> */
+                ]}
+                searchLabel='Name/Description'
+                searchPlaceholder='Search by name/description'
+                urlToRetrieveData={urlDifferentialExpressionExperimentResults + props.differentialExpressionAnalysis?.id + '/'}
+                updateWSKey='update_differential_expression_experiments'
+                mapFunction={(differentialExpressionAnalysis: any) => {
+                    return (
+                        <Table.Row key={differentialExpressionAnalysis.id as number}>
+                            <TableCellWithTitle value='differentialExpressionAnalysis.name' />
+                            <TableCellWithTitle value={differentialExpressionAnalysis.description} />
+                            <TableCell>
+                                <>hola</>
+                            </TableCell>
+                        </Table.Row>
+                    )
+                }}
+            />
+        </Modal>
+    )
+}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index 5695b735..fe7d6f76 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -7,7 +7,7 @@ import { TableCellWithTitle } from '../common/TableCellWithTitle'
 import { Alert } from '../common/Alert'
 import { ConfirmModal, CustomAlert, CustomAlertTypes, GenesColors, Nullable } from '../../utils/interfaces'
 import { DifferentialExpressionAnalysis, DifferentialExpressionAnalysisExperimentState } from './types'
-import { formatDateLocale, getDefaultAlertProps, getDefaultConfirmModal, getDjangoHeader, getExperimentStateObj } from '../../utils/util_functions'
+import { formatDateLocale, getDefaultAlertProps, getDefaultConfirmModal, getDjangoHeader, getExperimentStateObjDiffExperiment } from '../../utils/util_functions'
 import { SourcePopup } from '../pipeline/all-experiments-view/SourcePopup'
 import { PopupIcons } from '../common/PopupIcons'
 import { DeleteButton } from '../common/DeleteButton'
@@ -15,6 +15,7 @@ import { SwitchPublicButton } from '../common/SwitchPublicButton'
 import { StopExperimentButton } from '../pipeline/all-experiments-view/StopExperimentButton'
 import ky from 'ky'
 import { EditIcon } from '../common/EditIcon'
+import { DifferentialExpressionModalResults } from './DifferentialExpressionModalResults'
 
 declare const urlDifferentialExpressionList:string
 declare const urlDifferentialExpressionStop:string
@@ -25,6 +26,10 @@ interface DiferentialExpressionPanelState {
     modal: ConfirmModal
     stoppingExperiment: boolean
     experimentToEdit: Nullable<DifferentialExpressionAnalysis>
+    modalResult: {
+        differentialExpressionAnalysis: DifferentialExpressionAnalysis | null
+        isOpen: boolean
+    }
 }
 
 export const DiferentialExpressionPanel = () => {
@@ -32,7 +37,11 @@ export const DiferentialExpressionPanel = () => {
         alert: getDefaultAlertProps(),
         modal: getDefaultConfirmModal(),
         stoppingExperiment: false,
-        experimentToEdit: null
+        experimentToEdit: null,
+        modalResult: {
+            differentialExpressionAnalysis: null,
+            isOpen: false
+        }
     })
 
     const handleEdit = (differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
@@ -72,8 +81,8 @@ export const DiferentialExpressionPanel = () => {
      * @returns Default object for table's Filters
      */
     const getDefaultFilters = (): PaginationCustomFilter[] => {
-        const methodsOptions: DropdownItemProps[] = [{ id: 1, name: 'Lima' }, { id: 2, name: 'Deseq2' }].map((tag) => {
-            const id = tag.id as number
+        const methodsOptions: DropdownItemProps[] = [{ id: 'LIMMA', name: 'Lima' }, { id: 'DESEQ', name: 'Deseq2' }].map((tag) => {
+            const id = tag.id
             return { key: id, value: id, text: tag.name }
         })
 
@@ -84,6 +93,13 @@ export const DiferentialExpressionPanel = () => {
         ]
     }
 
+    const openInferenceResult = (differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
+        setState(prevState => ({
+            ...prevState,
+            modalResult: { differentialExpressionAnalysis, isOpen: true }
+        }))
+    }
+
     /**
      * Stop experiment
      * @param experimentId experiment to stop
@@ -210,8 +226,7 @@ export const DiferentialExpressionPanel = () => {
                         mapFunction={(differentialExpressionAnalysis: DifferentialExpressionAnalysis) => {
                             const isInProcess = differentialExpressionAnalysis.state === DifferentialExpressionAnalysisExperimentState.IN_PROCESS ||
                             differentialExpressionAnalysis.state === DifferentialExpressionAnalysisExperimentState.WAITING_FOR_QUEUE
-
-                            const experimentState = getExperimentStateObj(differentialExpressionAnalysis.state as any)
+                            const experimentState = getExperimentStateObjDiffExperiment(differentialExpressionAnalysis.state as any)
 
                             return (
                                 <Table.Row key={differentialExpressionAnalysis.id as number}>
@@ -271,7 +286,15 @@ export const DiferentialExpressionPanel = () => {
                                     </TableCell>
                                     <TableCell>
                                         {/* See results button */}
-
+                                        {differentialExpressionAnalysis.state !== DifferentialExpressionAnalysisExperimentState.COMPLETED && (
+                                            <Icon
+                                                name='chart area'
+                                                onClick={() => { openInferenceResult(differentialExpressionAnalysis) }}
+                                                className='clickable'
+                                                color='blue'
+                                                title='See results'
+                                            />
+                                        )}
                                         {/* Edit button */}
                                         <EditIcon
                                             editExperiment={() => handleEdit(differentialExpressionAnalysis)}
@@ -347,6 +370,13 @@ export const DiferentialExpressionPanel = () => {
                     }))
                 }}
             />
+            <DifferentialExpressionModalResults
+                isOpen={state.modalResult.isOpen} differentialExpressionAnalysis={state.modalResult.differentialExpressionAnalysis}
+                closeModal={() => setState(prevState => ({
+                    ...prevState,
+                    modalResult: { differentialExpressionAnalysis: null, isOpen: false }
+                }))}
+            />
         </Base>
     )
 }
diff --git a/src/frontend/static/frontend/src/components/differential-expression/types.ts b/src/frontend/static/frontend/src/components/differential-expression/types.ts
index 30f3ce9f..0b06e49d 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/types.ts
+++ b/src/frontend/static/frontend/src/components/differential-expression/types.ts
@@ -4,14 +4,17 @@ import { DjangoExperimentSource, DjangoUser } from '../../utils/django_interface
  * Possible states for experiment evaluation
  */
 export enum DifferentialExpressionAnalysisExperimentState {
-    WAITING_FOR_QUEUE = 1,
-    IN_PROCESS = 2,
-    COMPLETED = 3,
-    FINISHED_WITH_ERROR = 4,
+    COMPLETED = 1,
+    FINISHED_WITH_ERROR = 2,
+    IN_PROCESS = 3,
+    WAITING_FOR_QUEUE = 4,
     NO_SAMPLES_IN_COMMON = 5,
+    STOPPING = 6,
     STOPPED = 7,
     REACHED_ATTEMPTS_LIMIT = 8,
-    TIMEOUT_EXCEEDED = 9,
+    NO_FEATURES_FOUND = 9,
+    EMPTY_DATASET = 10,
+    TIMEOUT_EXCEEDED = 11,
 }
 
 export interface DifferentialExpressionAnalysis {
diff --git a/src/frontend/static/frontend/src/css/differential-expression.css b/src/frontend/static/frontend/src/css/differential-expression.css
index 3c92dd5f..bdda5ac3 100644
--- a/src/frontend/static/frontend/src/css/differential-expression.css
+++ b/src/frontend/static/frontend/src/css/differential-expression.css
@@ -15,4 +15,14 @@
     width: 100%;
     margin-top: 10px;
     margin-bottom: 10px;
+}
+.large-modal {
+    min-height: 92% !important;
+    width: 92% !important;
+}
+
+.space-modal:nth-child(1) {
+    display: flex !important;
+    flex-direction: column;
+    justify-content: space-between;
 }
\ No newline at end of file
diff --git a/src/frontend/static/frontend/src/utils/util_functions.ts b/src/frontend/static/frontend/src/utils/util_functions.ts
index ad3f8c4b..6ef982fd 100644
--- a/src/frontend/static/frontend/src/utils/util_functions.ts
+++ b/src/frontend/static/frontend/src/utils/util_functions.ts
@@ -5,6 +5,7 @@ import { TagType, DjangoTag, ExperimentState, ExperimentType, CorrelationMethod,
 import dayjs from 'dayjs'
 import countBy from 'lodash/countBy'
 import { MAX_FILE_SIZE_IN_MB_ERROR } from './constants'
+import { DifferentialExpressionAnalysisExperimentState } from '../components/differential-expression/types'
 
 /** User locale extracted from the browser. */
 const USER_LOCALE: readonly string[] | string = navigator.languages !== undefined && navigator.languages.length > 0
@@ -235,6 +236,92 @@ const getExperimentStateObj = (state: ExperimentState): StateIconInfo => {
     return stateIcon
 }
 
+/**
+ * Gets info about the state of a specific Experiment to display in the card
+ * @param state Experiment state
+ * @returns The corresponding info of the current experiment's state of a differential expressione
+ */
+const getExperimentStateObjDiffExperiment = (state: DifferentialExpressionAnalysisExperimentState): StateIconInfo => {
+    let stateIconDiffExp: StateIconInfo | null = null
+
+    switch (state) {
+        case DifferentialExpressionAnalysisExperimentState.COMPLETED:
+            stateIconDiffExp = {
+                iconName: 'check',
+                color: 'green',
+                loading: false,
+                title: 'The analysis is complete'
+            }
+            break
+        case DifferentialExpressionAnalysisExperimentState.FINISHED_WITH_ERROR:
+            stateIconDiffExp = {
+                iconName: 'times',
+                color: 'red',
+                loading: false,
+                title: 'The analysis has finished with errors. Try again'
+            }
+            break
+        case DifferentialExpressionAnalysisExperimentState.WAITING_FOR_QUEUE:
+            stateIconDiffExp = {
+                iconName: 'wait',
+                color: 'yellow',
+                loading: false,
+                title: 'The process of this analysis will start soon'
+            }
+            break
+        case DifferentialExpressionAnalysisExperimentState.NO_SAMPLES_IN_COMMON:
+            stateIconDiffExp = {
+                iconName: 'user outline',
+                color: 'red',
+                loading: false,
+                title: 'Datasets don\'t have samples in common'
+            }
+            break
+        case DifferentialExpressionAnalysisExperimentState.IN_PROCESS:
+            stateIconDiffExp = {
+                iconName: 'sync alternate',
+                color: 'yellow',
+                loading: true,
+                title: 'The analysis is being processed'
+            }
+            break
+        case DifferentialExpressionAnalysisExperimentState.STOPPING:
+            stateIconDiffExp = {
+                iconName: 'stop',
+                color: 'red',
+                loading: false,
+                title: 'The analysis was stopped'
+            }
+            break
+        case DifferentialExpressionAnalysisExperimentState.REACHED_ATTEMPTS_LIMIT:
+            stateIconDiffExp = {
+                iconName: 'undo',
+                color: 'red',
+                loading: false,
+                title: 'The analysis has failed several times. Try changing some parameters and try again'
+            }
+            break
+        case DifferentialExpressionAnalysisExperimentState.TIMEOUT_EXCEEDED:
+            stateIconDiffExp = {
+                iconName: 'wait',
+                color: 'red',
+                loading: false,
+                title: 'The analysis has reached the timeout limit. Try changing some parameters and try again'
+            }
+            break
+        default:
+            stateIconDiffExp = {
+                iconName: 'times',
+                color: 'red',
+                loading: false,
+                title: 'The analysis has finished with errors. Try again'
+            }
+            break
+    }
+
+    return stateIconDiffExp
+}
+
 /**
  * Gets info about an experiment's type to display in a Label
  * @param GEMType GEM FileType or Experiment to return its description
@@ -833,5 +920,6 @@ export {
     getFileTypeName,
     getInputFileCSVFirstColumnAllRows,
     getDefaultConfirmModal,
-    getDefaultAlertProps
+    getDefaultAlertProps,
+    getExperimentStateObjDiffExperiment,
 }
diff --git a/src/frontend/templates/frontend/differential-expression.html b/src/frontend/templates/frontend/differential-expression.html
index e0e493d3..cca9898a 100644
--- a/src/frontend/templates/frontend/differential-expression.html
+++ b/src/frontend/templates/frontend/differential-expression.html
@@ -26,6 +26,7 @@
             const downloadFileURL = "{% url 'download_user_file' %}"
             const urlDeleteExperiment = "{% url 'differential_expression_delete' %}"
             const urlUpdateExperiment = "{% url 'differential_expression_update' %}"
+            const urlDifferentialExpressionExperimentResults = "{% url 'differential_expression_results' %}"
         </script>
         {% render_bundle 'differentialExpression' 'js' %}
 {% endblock %}
\ No newline at end of file

From 6f74ae8ddcf3431bf31d30d47e9feb0766b4beda Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Sat, 8 Nov 2025 13:06:22 -0300
Subject: [PATCH 23/47] Changed deprecated prop

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 171a4801..e354cd0a 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-<img align="right" src="src/frontend/static/frontend/img/logo-readme.png" alt="Multiomix logo">
+<img style="float: right" src="src/frontend/static/frontend/img/logo-readme.png" alt="Multiomix logo">
 
 # Multiomix
 

From 634cafbb81072a7c440e3e588e6349ff0c5c120b Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Sat, 8 Nov 2025 13:07:19 -0300
Subject: [PATCH 24/47] Refactoring, fixed types and typos

---
 src/api_service/models.py                   |  8 +-
 src/api_service/websocket_functions.py      | 12 +--
 src/datasets_synchronization/admin.py       |  3 +-
 src/datasets_synchronization/models.py      |  2 +-
 src/datasets_synchronization/serializers.py | 15 ++--
 src/differential_expression/models.py       | 71 +++++++++--------
 src/differential_expression/serializers.py  | 85 ++++++++++-----------
 src/differential_expression/views.py        | 15 ++--
 8 files changed, 109 insertions(+), 102 deletions(-)

diff --git a/src/api_service/models.py b/src/api_service/models.py
index e18ec18e..8284560c 100644
--- a/src/api_service/models.py
+++ b/src/api_service/models.py
@@ -396,10 +396,8 @@ class Experiment(models.Model):
     # TODO: this can be stored in the Methylation type entity. Set the corresponding nullity in the new schema
     correlate_with_all_genes: bool = models.BooleanField(blank=False, null=False, default=True)
 
-    shared_institutions = models.ManyToManyField(Institution, blank=True,
-                                                 related_name='shared_correlation_analysis')
-    shared_users = models.ManyToManyField(User, blank=True,
-                                                 related_name='shared_users_correlation_analysis')
+    shared_institutions = models.ManyToManyField(Institution, blank=True, related_name='shared_correlation_analysis')
+    shared_users = models.ManyToManyField(User, blank=True, related_name='shared_users_correlation_analysis')
     is_public = models.BooleanField(blank=False, null=False, default=False)
 
     @property
@@ -417,7 +415,7 @@ def get_combination_class(self):
         """
         return get_combination_class(self.type)
 
-    def get_clinical_columns(self):
+    def get_clinical_columns(self) -> list[str]:
         """
         Gets a list of columns from the clinical data
         @return: List of fields in clinical data
diff --git a/src/api_service/websocket_functions.py b/src/api_service/websocket_functions.py
index 7825ec58..9fc51255 100644
--- a/src/api_service/websocket_functions.py
+++ b/src/api_service/websocket_functions.py
@@ -40,7 +40,7 @@ def send_update_cgds_studies_command():
 
 def send_update_biomarkers_command(user_id: int):
     """
-    Sends a message indicating that an Biomarker's state update has occurred
+    Sends a message indicating that a Biomarker's state update has occurred
     """
     user_group_name = f'notifications_{user_id}'
     message = {
@@ -51,7 +51,7 @@ def send_update_biomarkers_command(user_id: int):
 
 def send_update_user_file_command(user_id: int):
     """
-    Sends a message indicating that an user file's state update has occurred
+    Sends a message indicating that a user file's state update has occurred
     """
     user_group_name = f'notifications_{user_id}'
     message = {
@@ -119,9 +119,10 @@ def send_update_cluster_label_set_command(user_id: int):
     }
     send_message(user_group_name, message)
 
+
 def send_update_institutions_command(user_id: int):
     """
-    Sends a message indicating that a Institution state update has occurred
+    Sends a message indicating that an Institution state update has occurred
     @param user_id: Institution's user's id to send the WS message
     """
     user_group_name = f'notifications_{user_id}'
@@ -130,13 +131,14 @@ def send_update_institutions_command(user_id: int):
     }
     send_message(user_group_name, message)
 
+
 def send_update_user_for_institution_command(user_id: int):
     """
-    Sends a message indicating that a Institution_user state update has occurred
+    Sends a message indicating that an Institution_user state update has occurred
     @param user_id: Institution's user's id to send the WS message
     """
     user_group_name = f'notifications_{user_id}'
     message = {
         'command': 'update_user_for_institution'
     }
-    send_message(user_group_name, message)
\ No newline at end of file
+    send_message(user_group_name, message)
diff --git a/src/datasets_synchronization/admin.py b/src/datasets_synchronization/admin.py
index 670b8c4c..63341976 100644
--- a/src/datasets_synchronization/admin.py
+++ b/src/datasets_synchronization/admin.py
@@ -42,9 +42,9 @@ def delete_queryset(self, request, queryset):
                      'mirna_dataset__name', 'mrna_dataset__name')
 
 
-
 class SurvivalColumnsTupleAdmin(admin.ModelAdmin):
     """Useful for SurvivalColumnsTupleCGDSDataset and SurvivalColumnsTupleUserFile models."""
+
     @staticmethod
     @admin.display(description='CGDS Dataset')
     def dataset(obj: Union[SurvivalColumnsTupleCGDSDataset, SurvivalColumnsTupleUserFile]) -> str:
@@ -53,6 +53,7 @@ def dataset(obj: Union[SurvivalColumnsTupleCGDSDataset, SurvivalColumnsTupleUser
     list_display = ('pk', 'dataset', 'time_column', 'event_column')
     search_fields = ('time_column', 'event_column')
 
+
 # IMPORTANT: these models should be managed in the CGDS Panel in the frontend!
 admin.site.register(CGDSStudy, CGDSStudyAdmin)
 admin.site.register(CGDSDataset, CGDSDatasetAdmin)
diff --git a/src/datasets_synchronization/models.py b/src/datasets_synchronization/models.py
index 7888f2e6..2ed80a33 100644
--- a/src/datasets_synchronization/models.py
+++ b/src/datasets_synchronization/models.py
@@ -112,7 +112,7 @@ def study(self) -> Optional['CGDSDataset']:
 
     def __str__(self) -> str:
         study_name = self.study.name if self.study else '-'
-        return f'File: {self.file_path} | Col: {self.mongo_collection_name} | Assigned to study: {study_name}'
+        return f'PK: {self.pk} | File: {self.file_path} | Col: {self.mongo_collection_name} | Assigned to study: {study_name}'
 
     def __compute_number_of_row_and_samples_and_save(self) -> None:
         """
diff --git a/src/datasets_synchronization/serializers.py b/src/datasets_synchronization/serializers.py
index 26bd47fe..44501839 100644
--- a/src/datasets_synchronization/serializers.py
+++ b/src/datasets_synchronization/serializers.py
@@ -28,7 +28,7 @@ class Meta:
         fields = ['id', 'time_column', 'event_column']
 
     def get_fields(self, *args, **kwargs):
-        fields = super(SurvivalColumnsTupleCGDSSimpleSerializer, self).get_fields(*args, **kwargs)
+        fields = super(SurvivalColumnsTupleCGDSSimpleSerializer, self).get_fields()
         request = self.context.get('request', None)
         if request and getattr(request, 'method', None) == "POST":
             fields['id'].required = False
@@ -123,9 +123,9 @@ def __check_collection_name(mongo_collection_name: str, editing_cgds_dataset_id:
             })
 
     def __update_cgds_dataset(
-        self,
-        cgds_dataset_instance: CGDSDataset,
-        validated_data_pop
+            self,
+            cgds_dataset_instance: CGDSDataset,
+            validated_data_pop
     ) -> Optional[CGDSDataset]:
         """
         Updates a CGDSDataset instance from a request data
@@ -186,10 +186,9 @@ def __update_survival_columns(cgds_dataset_instance: CGDSDataset, validated_data
                 # If there's an existing id, updates the element
                 if 'id' in survival_column:
                     try:
-                        survival_column_obj: SurvivalColumnsTupleCGDSDataset = SurvivalColumnsTupleCGDSDataset. \
-                            objects.get(
-                                pk=survival_column['id']
-                            )
+                        survival_column_obj: SurvivalColumnsTupleCGDSDataset = SurvivalColumnsTupleCGDSDataset.objects.get(
+                            pk=survival_column['id']
+                        )
                         survival_column_obj.time_column = survival_column['time_column']
                         survival_column_obj.event_column = survival_column['event_column']
                         survival_column_obj.save()
diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index 420a35f5..d63b5f38 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -6,11 +6,12 @@
 import pandas as pd
 import numpy as np
 import math
-from django.db.models import Q
+from django.db.models import Q, QuerySet
 
 from api_service.websocket_functions import send_update_differential_expression_experiments_command
 from common.constants import PATIENT_ID_COLUMN
 
+
 class DifferentialExpressionSource(models.Model):
     """
     Represents a data source for differential expression experiments.
@@ -101,8 +102,8 @@ class DifferentialExpressionClinicalSource(DifferentialExpressionSource):
     """
     extra_cgds_dataset = models.ForeignKey(
         'datasets_synchronization.CGDSDataset',
-        on_delete=models.CASCADE, 
-        blank=True, 
+        on_delete=models.CASCADE,
+        blank=True,
         null=True,
         related_name='differential_expression_clinical_sources_extra'
     )
@@ -135,11 +136,11 @@ def get_attributes(self) -> List[str]:
         if self.cgds_dataset:
             first_clinical_source_columns = self.cgds_dataset.get_column_names()
             columns_distinct.update(first_clinical_source_columns)
-        
+
         if self.extra_cgds_dataset:
             second_clinical_source_columns = self.extra_cgds_dataset.get_column_names()
             columns_distinct.update(second_clinical_source_columns)
-        
+
         # Remove special columns
         special_columns = ['SAMPLE_ID', 'PATIENT_ID']
         for column_to_remove in special_columns:
@@ -168,7 +169,7 @@ def get_specific_samples_and_attributes(
             result = df[clinical_attributes].to_numpy()
             return result if len(clinical_attributes) > 1 else result[:, 0]
 
-    def _get_cgds_datasets_joined_df(self) -> pd.DataFrame:
+    def _get_cgds_datasets_joined_df(self) -> pd.DataFrame | None:
         """
         Gets a joined DataFrame from both CGDS datasets (patient and sample data)
         @return: Joined DataFrame
@@ -185,6 +186,8 @@ def _get_cgds_datasets_joined_df(self) -> pd.DataFrame:
 
             return df1.join(df2)
 
+        return None
+
     def get_df(self, only_matching: bool = False) -> pd.DataFrame:
         """
         Generates a DataFrame from the clinical source
@@ -210,15 +213,18 @@ class DifferentialExpressionExperimentState(models.IntegerChoices):
     EMPTY_DATASET = 10
     TIMEOUT_EXCEEDED = 11
 
+
 class DifferentialExpressionTool(models.TextChoices):
     """Tool choices for differential expression analysis."""
     DESEQ = 'DESEQ'
     LIMMA = 'LIMMA'
 
+
 class DifferentialExpressionExperiment(models.Model):
     """
     Model to create and manage differential expression data.
     """
+    results: QuerySet['DifferentialExpressionExperimentResult']
 
     name = models.CharField(max_length=300)
     description = models.TextField(blank=True, null=True)
@@ -226,17 +232,17 @@ class DifferentialExpressionExperiment(models.Model):
     # Clinical and mRNA sources
     # These are used to link the experiment to the clinical and mRNA data sources
     clinical_source = models.ForeignKey(
-        'DifferentialExpressionClinicalSource', 
-        on_delete=models.CASCADE, 
+        'DifferentialExpressionClinicalSource',
+        on_delete=models.CASCADE,
         null=False,
-        blank=False, 
+        blank=False,
         related_name='differential_expression_experiments_as_clinical'
     )
 
     mrna_source = models.ForeignKey(
-        'DifferentialExpressionSource', 
-        on_delete=models.CASCADE, 
-        null=False, 
+        'DifferentialExpressionSource',
+        on_delete=models.CASCADE,
+        null=False,
         blank=False,
         related_name='differential_expression_experiments_as_mrna'
     )
@@ -257,8 +263,8 @@ class DifferentialExpressionExperiment(models.Model):
     threshold = models.FloatField(default=0.0001, blank=False, null=False)
 
     top = models.IntegerField(
-        default=100, 
-        blank=False, 
+        default=100,
+        blank=False,
         null=False,
         help_text='Number of significant results to keep (max 1000)'
     )
@@ -274,11 +280,12 @@ class DifferentialExpressionExperiment(models.Model):
         default=DifferentialExpressionExperimentState.WAITING_FOR_QUEUE,
         help_text='Current state of the differential expression experiment'
     )
-    
+
     # Timestamp fields
-    created_at = models.DateTimeField(auto_now_add=True, null=True, blank=True, help_text='When the experiment was created')
+    created_at = models.DateTimeField(auto_now_add=True, null=True, blank=True,
+                                      help_text='When the experiment was created')
     updated_at = models.DateTimeField(auto_now=True, help_text='When the experiment was last updated')
-    
+
     # User and sharing information
     # This is used to track the user who created the experiment and to share it with other users or institutions
     user = models.ForeignKey(get_user_model(), on_delete=models.CASCADE)
@@ -316,7 +323,7 @@ def save_results(self, dataframe):
         """
         # Clear existing results
         self.results.all().delete()
-        
+
         # Create new result records
         results_to_create = []
         for gene_name, row in dataframe.iterrows():
@@ -329,7 +336,7 @@ def safe_float(value, default=0.0):
                     return float(value)
                 except (ValueError, TypeError):
                     return default
-            
+
             result = DifferentialExpressionExperimentResult(
                 experiment=self,
                 gene=str(gene_name),  # The gene identifier from the DataFrame index
@@ -341,10 +348,10 @@ def safe_float(value, default=0.0):
                 b_statistic=safe_float(row.get('B', 0.0), 0.0)
             )
             results_to_create.append(result)
-        
+
         # Bulk create for efficiency
         DifferentialExpressionExperimentResult.objects.bulk_create(results_to_create)
-    
+
     def get_results_dataframe(self):
         """
         Retrieve results as a pandas DataFrame.
@@ -352,7 +359,7 @@ def get_results_dataframe(self):
         results = self.results.all()
         if not results.exists():
             return None
-            
+
         data = []
         for result in results:
             data.append({
@@ -364,11 +371,11 @@ def get_results_dataframe(self):
                 't': result.t_statistic,
                 'B': result.b_statistic
             })
-        
+
         df = pd.DataFrame(data)
         df.set_index('gene', inplace=True)
         return df
-    
+
     def get_significant_genes(self, p_value_threshold=0.05, log_fc_threshold=1.0):
         """
         Get significantly differentially expressed genes.
@@ -380,7 +387,7 @@ def get_significant_genes(self, p_value_threshold=0.05, log_fc_threshold=1.0):
         Returns:
             QuerySet: QuerySet of DifferentialExpressionExperimentResult objects meeting the criteria
         """
-        
+
         return self.results.filter(
             Q(adj_p_val__lte=p_value_threshold) &
             (Q(log_fc__gte=log_fc_threshold) | Q(log_fc__lte=-log_fc_threshold))
@@ -401,10 +408,10 @@ class DifferentialExpressionExperimentResult(models.Model):
     """
     Model to store individual differential expression results for each gene.
     """
-    
+
     experiment = models.ForeignKey(
-        'DifferentialExpressionExperiment', 
-        on_delete=models.CASCADE, 
+        'DifferentialExpressionExperiment',
+        on_delete=models.CASCADE,
         related_name='results'
     )
     gene = models.CharField(max_length=100, help_text='Gene identifier')
@@ -414,7 +421,7 @@ class DifferentialExpressionExperimentResult(models.Model):
     log_fc = models.FloatField(help_text='Log fold change')
     t_statistic = models.FloatField(help_text='t-statistic from the test')
     b_statistic = models.FloatField(help_text='B-statistic (log-odds of differential expression)')
-    
+
     class Meta:
         unique_together = ('experiment', 'gene')
         indexes = [
@@ -422,12 +429,12 @@ class Meta:
             models.Index(fields=['experiment', 'log_fc']),
             models.Index(fields=['gene']),
         ]
-    
+
     def __str__(self):
         return f"{self.gene} - {self.experiment.name}"
-    
+
     @property
     def is_significant(self, p_threshold=0.05, fc_threshold=1.0):
         """Check if this gene is significantly differentially expressed."""
-        return (self.adj_p_val <= p_threshold and 
+        return (self.adj_p_val <= p_threshold and
                 abs(self.log_fc) >= fc_threshold)
diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index d7d2d8fc..fda581d5 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -1,17 +1,17 @@
-from rest_framework import serializers
 from django.contrib.auth.models import User
-from institutions.models import Institution
+from rest_framework import serializers
+
 from api_service.serializers import ExperimentSourceSerializer, ExperimentClinicalSourceSerializer
 from differential_expression.models import (
     DifferentialExpressionExperiment,
-    DifferentialExpressionExperimentResult,
-    DifferentialExpressionClinicalSource
+    DifferentialExpressionExperimentResult
 )
-
+from institutions.models import Institution
 
 
 class UserSimpleSerializer(serializers.ModelSerializer):
     """Simple serializer for User model."""
+
     class Meta:
         model = User
         fields = ['id', 'username', 'first_name', 'last_name', 'email']
@@ -20,6 +20,7 @@ class Meta:
 
 class InstitutionSimpleSerializer(serializers.ModelSerializer):
     """Simple serializer for Institution model."""
+
     class Meta:
         model = Institution
         fields = ['id', 'name']
@@ -31,14 +32,14 @@ class DifferentialExpressionExperimentResultSerializer(serializers.ModelSerializ
     Serializer for Differential Expression Experiment Results.
     """
     is_significant = serializers.SerializerMethodField()
-    
+
     class Meta:
         model = DifferentialExpressionExperimentResult
-        fields = ['id', 'gene', 'ave_expr', 'p_value', 'adj_p_val', 'log_fc', 't_statistic', 'b_statistic', 'is_significant'
-        ]
-        read_only_fields = ['id']
-    
-    def get_is_significant(self, obj):
+        fields = ['id', 'gene', 'ave_expr', 'p_value', 'adj_p_val', 'log_fc', 't_statistic', 'b_statistic',
+                  'is_significant']
+
+    @staticmethod
+    def get_is_significant(obj):
         """Check if this gene is significantly differentially expressed."""
         return obj.adj_p_val <= 0.05 and abs(obj.log_fc) >= 1.0
 
@@ -61,16 +62,16 @@ class DifferentialExpressionExperimentListSerializer(serializers.ModelSerializer
     class Meta:
         model = DifferentialExpressionExperiment
         fields = [
-            'id',              # Experiment ID
-            'user',            # User ID (compatible with frontend expectations)
-            'name',            # Experiment name
-            'description',     # Experiment description
-            'created_at',      # Creation date
-            'state',           # Experiment state
-            'state_display',   # Human-readable state
-            'clinical_source', # Clinical data source (ExperimentClinicalSourceSerializer)
-            'mrna_source',     # mRNA data source (ExperimentSourceSerializer)
-            'is_public',        # Public visibility flag
+            'id',  # Experiment ID
+            'user',  # User ID (compatible with frontend expectations)
+            'name',  # Experiment name
+            'description',  # Experiment description
+            'created_at',  # Creation date
+            'state',  # Experiment state
+            'state_display',  # Human-readable state
+            'clinical_source',  # Clinical data source (ExperimentClinicalSourceSerializer)
+            'mrna_source',  # mRNA data source (ExperimentSourceSerializer)
+            'is_public',  # Public visibility flag
             'tool'
         ]
         read_only_fields = [
@@ -87,9 +88,9 @@ class DifferentialExpressionExperimentSerializer(serializers.ModelSerializer):
     mrna_source = ExperimentSourceSerializer(read_only=True)
 
     # Computed fields
-    has_results = serializers.SerializerMethodField()
-    results_count = serializers.SerializerMethodField()
-    significant_genes_count = serializers.SerializerMethodField()
+    has_results = serializers.SerializerMethodField(method_name='get_has_results')
+    results_count = serializers.SerializerMethodField(method_name='get_results_count')
+    significant_genes_count = serializers.SerializerMethodField(method_name='get_significant_genes_count')
     state_display = serializers.CharField(source='get_state_display', read_only=True)
 
     class Meta:
@@ -101,30 +102,24 @@ class Meta:
             'has_results', 'results_count', 'significant_genes_count'
         ]
         read_only_fields = [
-            'id', 'execution_time', 'created_at', 'updated_at', 
+            'id', 'execution_time', 'created_at', 'updated_at',
             'has_results', 'results_count', 'significant_genes_count'
         ]
-    
-    def get_has_results(self, obj):
+
+    @staticmethod
+    def get_has_results(obj: DifferentialExpressionExperiment) -> bool:
         """Check if the experiment has results."""
-        try:
-            return obj.results.exists()
-        except:
-            return False
-    
-    def get_results_count(self, obj):
+        return obj.results.exists()
+
+    @staticmethod
+    def get_results_count(obj: DifferentialExpressionExperiment) -> int:
         """Get the total number of genes in results."""
-        try:
-            return obj.results.count()
-        except:
-            return 0
-    
-    def get_significant_genes_count(self, obj):
+        return obj.results.count()
+
+    @staticmethod
+    def get_significant_genes_count(obj: DifferentialExpressionExperiment) -> int:
         """Get the number of significant genes (adj.P.Val <= 0.05 and |logFC| >= 1.0)."""
-        try:
-            return obj.get_significant_genes().count()
-        except:
-            return 0
+        return obj.get_significant_genes().count()
 
 
 class DifferentialExpressionExperimentDetailSerializer(DifferentialExpressionExperimentSerializer):
@@ -134,11 +129,11 @@ class DifferentialExpressionExperimentDetailSerializer(DifferentialExpressionExp
     """
     shared_users = UserSimpleSerializer(many=True, read_only=True)
     shared_institutions = InstitutionSimpleSerializer(many=True, read_only=True)
-    
+
     class Meta(DifferentialExpressionExperimentSerializer.Meta):
         fields = DifferentialExpressionExperimentSerializer.Meta.fields + [
             'shared_users', 'shared_institutions', 'task_id', 'attempt'
         ]
         read_only_fields = DifferentialExpressionExperimentSerializer.Meta.read_only_fields + [
             'task_id', 'attempt'
-        ]
\ No newline at end of file
+        ]
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index cd8ad675..735c71a0 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -1,3 +1,4 @@
+import logging
 from typing import Optional, Dict, Tuple, List
 
 import numpy as np
@@ -29,7 +30,7 @@
 from differential_expression.serializers import (
     DifferentialExpressionExperimentDetailSerializer,
     DifferentialExpressionExperimentResultSerializer,
-    DifferentialExpressionExperimentSerializer, DifferentialExpressionExperimentListSerializer,
+    DifferentialExpressionExperimentListSerializer,
 )
 from user_files.models import UserFile
 from user_files.models_choices import FileType
@@ -374,7 +375,8 @@ class GetCommonSamplesDifferentialExperiment(APIView):
 
     permission_classes = [permissions.IsAuthenticated]
 
-    def get(self, request: Request):
+    @staticmethod
+    def get(request: Request):
         mrna_source_id = request.GET.get('mRNASourceId')
         mrna_source_type = request.GET.get('mRNASourceType')
         clinical_source_id = request.GET.get('clinicalSourceId')
@@ -480,6 +482,7 @@ def post(request: Request):
         # Formats to JSON the ResponseStatus object
         return encode_json_response_status(response)
 
+
 class ToggleDiffExperimentPublicView(APIView):
     """
     API endpoint to toggle the 'is_public' field of an experiment.
@@ -487,7 +490,8 @@ class ToggleDiffExperimentPublicView(APIView):
     """
     permission_classes = [permissions.IsAuthenticated]
 
-    def post(self, request):
+    @staticmethod
+    def post(request):
         """
         Toggle the 'is_public' field of the experiment.
         """
@@ -507,6 +511,7 @@ def post(self, request):
             {"id": experiment.id, "is_public": experiment.is_public}
         )
 
+
 class DifferentialExpressionUpdate(APIView):
     """
     Endpoint to update name and description of a differential expression experiment.
@@ -613,9 +618,9 @@ def delete(request: Request, pk: int):
                 async_res = AbortableAsyncResult(experiment.task_id)
                 if async_res.state in ['PENDING', 'STARTED', 'RETRY']:
                     async_res.abort()
-            except Exception:
+            except Exception as ex:
                 # If we can't abort, continue with deletion anyway since state shows it's not running
-                pass
+                logging.exception(ex)
 
         # Delete the experiment (cascade will delete related objects)
         experiment.delete()

From a6733d25cc7f41bd52552ebaba91a2313bfdd8d9 Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Sat, 8 Nov 2025 13:07:27 -0300
Subject: [PATCH 25/47] Fixed bug with serializer + Refactoring

---
 src/datasets_synchronization/serializers.py | 28 +++++++++------------
 1 file changed, 12 insertions(+), 16 deletions(-)

diff --git a/src/datasets_synchronization/serializers.py b/src/datasets_synchronization/serializers.py
index 44501839..337e716f 100644
--- a/src/datasets_synchronization/serializers.py
+++ b/src/datasets_synchronization/serializers.py
@@ -308,21 +308,17 @@ def update(self, instance: CGDSStudy, validated_data):
 
 
 class SimpleCGDSDatasetSerializer(serializers.ModelSerializer):
+    """CGDSDataset serializer with few fields for list views."""
+    name = serializers.CharField(source='study.name', read_only=True)
+    description = serializers.CharField(source='study.description', read_only=True)
+    version = serializers.CharField(source='study.version', read_only=True)
+    file_obj = serializers.SerializerMethodField(method_name='get_file_obj')
+
     class Meta:
         model = CGDSDataset
-        fields = []
-
-    def to_representation(self, instance):
-        # Gets the file content for user_file
-        data = super(SimpleCGDSDatasetSerializer, self).to_representation(instance)
-
-        # Serialize the study
-        study = instance.study
-        data['name'] = study.name
-        data['description'] = study.description
-        data['version'] = study.version
-        data['date_last_synchronization'] = instance.date_last_synchronization
-        data['file_type'] = instance.file_type
-        data['file_obj'] = None
-
-        return data
+        fields = ['id', 'name', 'description', 'version', 'date_last_synchronization', 'file_type', 'file_obj']
+
+    @staticmethod
+    def get_file_obj(_instance: CGDSDataset):
+        """Returns None to avoid sending the file in list views."""
+        return None

From 09d9dc2463bd688feb1521912f15e75f7b794701 Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Sat, 8 Nov 2025 13:07:52 -0300
Subject: [PATCH 26/47] Removed checking optional description field to disabled
 submitting a DifferentialExpression experiment

---
 .../differential-expression/DifferentialExpressionForm.tsx       | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
index e356ad87..3f7a83ef 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionForm.tsx
@@ -577,7 +577,6 @@ export const DifferentialExpressionForm = (props: DifferentialExpressionFormProp
      */
     const submitDisabled = (form.differentialExpressionName.trim() === '' ||
             form.clinicalAttribute.trim() === '' ||
-            form.differentialExpressionDescription.trim() === '' ||
             isEqual(form.mRNASource, () => getDefaultSource()) ||
             isEqual(form.clinicalSource, () => getDefaultSource())
     ) && !(form.isEditing && form.differentialExpressionName.trim().length !== 0 && form.differentialExpressionDescription.trim().length !== 0)

From 020410afe34d9e770bc5d6b26fe597d993030b0f Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Sat, 8 Nov 2025 13:08:04 -0300
Subject: [PATCH 27/47] Removed unused packages

---
 src/frontend/static/frontend/package-lock.json | 17 -----------------
 1 file changed, 17 deletions(-)

diff --git a/src/frontend/static/frontend/package-lock.json b/src/frontend/static/frontend/package-lock.json
index 1b114777..e5b30b61 100644
--- a/src/frontend/static/frontend/package-lock.json
+++ b/src/frontend/static/frontend/package-lock.json
@@ -4883,23 +4883,6 @@
         "url": "https://github.com/sponsors/gregberge"
       }
     },
-    "node_modules/@swc/helpers": {
-      "version": "0.5.15",
-      "resolved": "https://registry.npmjs.org/@swc/helpers/-/helpers-0.5.15.tgz",
-      "integrity": "sha512-JQ5TuMi45Owi4/BIMAJBoSQoOJu12oOk/gADqlcUL9JEdHB8vyjUSsxqeNXnmXHjYKMi2WcYtezGEEhqUI/E2g==",
-      "dev": true,
-      "optional": true,
-      "dependencies": {
-        "tslib": "^2.8.0"
-      }
-    },
-    "node_modules/@swc/helpers/node_modules/tslib": {
-      "version": "2.8.1",
-      "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.8.1.tgz",
-      "integrity": "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w==",
-      "dev": true,
-      "optional": true
-    },
     "node_modules/@tootallnate/once": {
       "version": "1.1.2",
       "resolved": "https://registry.npmjs.org/@tootallnate/once/-/once-1.1.2.tgz",

From 396c4c59cb64aced65d814761d11ecaf03e5f461 Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Mon, 10 Nov 2025 10:10:14 -0300
Subject: [PATCH 28/47] Upgraded urllib3 to prevent "SSL: WRONG_VERSION_NUMBER
 ON PYTHON REQUEST" error

---
 config/requirements.txt        | 3 ++-
 config/requirements_celery.txt | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/config/requirements.txt b/config/requirements.txt
index 223b75ca..1279b8de 100644
--- a/config/requirements.txt
+++ b/config/requirements.txt
@@ -28,4 +28,5 @@ scipy==1.13.0
 statsmodels==0.14.2
 xlrd==2.0.1
 openpyxl==3.1.5
-rpy2==3.6.1
\ No newline at end of file
+rpy2==3.6.1
+urllib3==2.5.0
\ No newline at end of file
diff --git a/config/requirements_celery.txt b/config/requirements_celery.txt
index c69a236b..5c6b30bc 100644
--- a/config/requirements_celery.txt
+++ b/config/requirements_celery.txt
@@ -25,4 +25,5 @@ scipy==1.13.0
 statsmodels==0.14.2
 xlrd==2.0.1
 openpyxl==3.1.5
-rpy2==3.6.1
\ No newline at end of file
+rpy2==3.6.1
+urllib3==2.5.0
\ No newline at end of file

From 5cb81a73cf8d9dba1308945d3c7634b322256c7e Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Thu, 20 Nov 2025 22:48:21 -0300
Subject: [PATCH 29/47] Normalize mRNA dataset column names to match SAMPLE_IDs

Added logic to normalize mRNA dataset column names by extracting their base names, ensuring they match the normalized SAMPLE_IDs from clinical metadata. This improves consistency and accuracy when filtering and renaming columns for downstream analysis.
---
 src/differential_expression/service.py | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/src/differential_expression/service.py b/src/differential_expression/service.py
index 79687c4a..6480e209 100644
--- a/src/differential_expression/service.py
+++ b/src/differential_expression/service.py
@@ -251,11 +251,25 @@ def _process_mrna_data(self) -> None:
         # Antes de la intersección, normalizar los SAMPLE_ID extrayendo solo la parte base
         self.clinical_df['SAMPLE_ID'] = self.clinical_df['SAMPLE_ID'].str.rsplit('.', n=1).str[0]
 
+        # Normalizar también las columnas del mrna_dataset para machear con SAMPLE_ID
+        # Crear un mapeo de columnas normalizadas a columnas originales
+        normalized_columns = {}
+        for col in mrna_dataset.columns:
+            if col != 'Standard_Symbol':
+                # Extraer la parte base del nombre de la columna
+                normalized_col = col.rsplit('.', 1)[0] if '.' in col else col
+                normalized_columns[col] = normalized_col
+
         # Obtener valores de SAMPLE_ID del DataFrame de metadatos
-        valid_columns = list(set(mrna_dataset.columns) & set(self.clinical_df['SAMPLE_ID']))
-        
+        valid_sample_ids = set(self.clinical_df['SAMPLE_ID'])
+        valid_columns = [col for col, norm_col in normalized_columns.items() if norm_col in valid_sample_ids]
+
         # Filtrar el dataset de RNA-Seq para mantener solo las columnas válidas
         mrna_dataset = mrna_dataset[['Standard_Symbol'] + valid_columns]
+
+        # Renombrar las columnas para que coincidan con los SAMPLE_ID normalizados
+        rename_mapping = {col: normalized_columns[col] for col in valid_columns}
+        mrna_dataset = mrna_dataset.rename(columns=rename_mapping)
         
         # Eliminar filas con NA en los datos de expresión génica
         # Eliminar filas donde Standard_Symbol es NA

From b7aa7f9a1155bdc6037f0c42f2329b391e1814f9 Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Fri, 28 Nov 2025 20:29:55 -0300
Subject: [PATCH 30/47] push to check bugs in serializer

---
 src/differential_expression/serializers.py    | 16 ++---
 src/differential_expression/views.py          |  8 +--
 .../DifferentialExpressionModalResults.tsx    | 58 +++++++++++++++----
 .../DifferentialExpressionPanel.tsx           | 54 +++++++++--------
 .../differential-expression/types.ts          | 12 ++++
 .../frontend/src/utils/util_functions.ts      |  8 +++
 6 files changed, 104 insertions(+), 52 deletions(-)

diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index fda581d5..691c8aa9 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -122,18 +122,14 @@ def get_significant_genes_count(obj: DifferentialExpressionExperiment) -> int:
         return obj.get_significant_genes().count()
 
 
-class DifferentialExpressionExperimentDetailSerializer(DifferentialExpressionExperimentSerializer):
+class DifferentialExpressionExperimentDetailSerializer(serializers.ModelSerializer):
     """
     Detailed serializer for Differential Expression Experiment (Detail view).
     Includes additional information like shared users and institutions.
     """
-    shared_users = UserSimpleSerializer(many=True, read_only=True)
-    shared_institutions = InstitutionSimpleSerializer(many=True, read_only=True)
+    #shared_users = UserSimpleSerializer(many=True, read_only=True)
+    #shared_institutions = InstitutionSimpleSerializer(many=True, read_only=True)
 
-    class Meta(DifferentialExpressionExperimentSerializer.Meta):
-        fields = DifferentialExpressionExperimentSerializer.Meta.fields + [
-            'shared_users', 'shared_institutions', 'task_id', 'attempt'
-        ]
-        read_only_fields = DifferentialExpressionExperimentSerializer.Meta.read_only_fields + [
-            'task_id', 'attempt'
-        ]
+    class Meta:#DifferentialExpressionExperimentSerializer.Meta):
+        fields = '__all__'
+        model = DifferentialExpressionExperimentResult
\ No newline at end of file
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 735c71a0..816c55d0 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -112,14 +112,13 @@ class DifferentialExpressionDetail(generics.RetrieveAPIView):
     Endpoint to retrieve a differential expression experiment.
     """
 
-    def get_object(self) -> DifferentialExpressionExperiment:
+    def get_queryset(self) -> DifferentialExpressionExperiment:
         """
         Retrieve the differential expression experiment by its ID.
         """
         user = self.request.user
         experiment_id = self.kwargs.get('pk')
         experiment = get_object_or_404(DifferentialExpressionExperiment, pk=experiment_id)
-
         # Check if the user has access to the experiment
         if not (experiment.is_public or
                 experiment.user == user or
@@ -127,8 +126,9 @@ def get_object(self) -> DifferentialExpressionExperiment:
                 experiment.shared_users.filter(id=user.id).exists()):
             raise ValidationError('You do not have permission to access this experiment.')
 
-        return experiment
-
+        return experiment.results.all()
+    filter_backends = [filters.SearchFilter, filters.OrderingFilter, DjangoFilterBackend]
+    search_fields = ['gene']
     serializer_class = DifferentialExpressionExperimentDetailSerializer
     permission_classes = [permissions.IsAuthenticated]
 
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
index 1d3d842e..118633b3 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
@@ -1,5 +1,5 @@
 import React from 'react'
-import { DifferentialExpressionAnalysis } from './types'
+import { DifferentialExpressionAnalysis, DiffExpExperimentDetail } from './types'
 import { Icon, Modal, Table, TableCell } from 'semantic-ui-react'
 import { TableCellWithTitle } from '../common/TableCellWithTitle'
 import { PaginatedTable } from '../common/PaginatedTable'
@@ -23,11 +23,18 @@ export const DifferentialExpressionModalResults = (props: DifferentialExpression
             className='space-modal large-modal'
             onClose={props.closeModal}
         >
-            <PaginatedTable<DifferentialExpressionAnalysis>
+            <PaginatedTable<DiffExpExperimentDetail>
                 headerTitle='Differential Expressions experiment result'
                 headers={[
-                    { name: 'Name', serverCodeToSort: 'name', width: 3 },
-                    { name: 'Description', serverCodeToSort: 'description', width: 4 },
+                    { name: 'Gene', serverCodeToSort: 'gene' },
+                    { name: 'adj_p_val', serverCodeToSort: 'adj_p_val' },
+                    { name: 'ave_expr', serverCodeToSort: 'ave_expr' },
+                    { name: 'b_statistic', serverCodeToSort: 'b_statistic' },
+                    { name: 'log_fc', serverCodeToSort: 'log_fc' },
+                    { name: 'is_significant', serverCodeToSort: 'is_significant' },
+                    { name: 'p_value', serverCodeToSort: 'p_value' },
+                    { name: 't_statistic', serverCodeToSort: 't_statistic' },
+
                 ]}
                 defaultSortProp={{ sortField: 'created_at', sortOrderAscendant: false }}
                 customFilters={undefined}
@@ -43,17 +50,48 @@ export const DifferentialExpressionModalResults = (props: DifferentialExpression
                         </Button>
                     </Form.Field> */
                 ]}
-                searchLabel='Name/Description'
-                searchPlaceholder='Search by name/description'
+                searchLabel='Gene'
+                searchPlaceholder='Search by Gene'
                 urlToRetrieveData={urlDifferentialExpressionExperimentResults + props.differentialExpressionAnalysis?.id + '/'}
                 updateWSKey='update_differential_expression_experiments'
-                mapFunction={(differentialExpressionAnalysis: any) => {
+                mapFunction={(differentialExpressionAnalysis: DiffExpExperimentDetail) => {
                     return (
                         <Table.Row key={differentialExpressionAnalysis.id as number}>
-                            <TableCellWithTitle value='differentialExpressionAnalysis.name' />
-                            <TableCellWithTitle value={differentialExpressionAnalysis.description} />
+                            <TableCellWithTitle value={differentialExpressionAnalysis.gene} />
+                            <TableCellWithTitle value={differentialExpressionAnalysis.adj_p_val.toString()} />
+                            <TableCell>
+                                {differentialExpressionAnalysis.ave_expr}
+                            </TableCell>
+                            <TableCell>
+                                {differentialExpressionAnalysis.b_statistic}
+                            </TableCell>
+                            <TableCell>
+                                {differentialExpressionAnalysis.log_fc}
+                            </TableCell>
+                            <TableCell textAlign='center'>
+                                {
+                                    differentialExpressionAnalysis.is_significant
+                                        ? (
+                                            <Icon
+                                                title='Is significant'
+                                                name='check'
+                                                color='green'
+                                            />
+                                        )
+                                        : (
+                                            <Icon
+                                                title='Is not significant'
+                                                name='close'
+                                                color='red'
+                                            />
+                                        )
+                                }
+                            </TableCell>
+                            <TableCell>
+                                {differentialExpressionAnalysis.p_value}
+                            </TableCell>
                             <TableCell>
-                                <>hola</>
+                                {differentialExpressionAnalysis.t_statistic}
                             </TableCell>
                         </Table.Row>
                     )
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index fe7d6f76..aa70ea7c 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -244,25 +244,21 @@ export const DiferentialExpressionPanel = () => {
                                     </TableCell>
                                     <TableCell>
                                         {/* Download mRNA */}
-                                        {
-                                            differentialExpressionAnalysis.mrna_source.user_file && (
-                                                <>
-                                                    <SourcePopup
-                                                        source={differentialExpressionAnalysis.mrna_source}
-                                                        iconName='file'
-                                                        iconColor={GenesColors.MRNA}
-                                                        downloadButtonTitle='Download source mRNA file'
-                                                    />
+                                        <>
+                                            <SourcePopup
+                                                source={differentialExpressionAnalysis.mrna_source}
+                                                iconName='file'
+                                                iconColor={GenesColors.MRNA}
+                                                downloadButtonTitle='Download source mRNA file'
+                                            />
 
-                                                    <SourcePopup
-                                                        source={differentialExpressionAnalysis.clinical_source}
-                                                        iconName='file alternate'
-                                                        iconColor={GenesColors.CLINICAL}
-                                                        downloadButtonTitle='Download Clinical source file'
-                                                    />
-                                                </>
-                                            )
-                                        }
+                                            <SourcePopup
+                                                source={differentialExpressionAnalysis.clinical_source}
+                                                iconName='file alternate'
+                                                iconColor={GenesColors.CLINICAL}
+                                                downloadButtonTitle='Download Clinical source file'
+                                            />
+                                        </>
 
                                     </TableCell>
                                     <TableCell textAlign='center'>
@@ -286,15 +282,17 @@ export const DiferentialExpressionPanel = () => {
                                     </TableCell>
                                     <TableCell>
                                         {/* See results button */}
-                                        {differentialExpressionAnalysis.state !== DifferentialExpressionAnalysisExperimentState.COMPLETED && (
-                                            <Icon
-                                                name='chart area'
-                                                onClick={() => { openInferenceResult(differentialExpressionAnalysis) }}
-                                                className='clickable'
-                                                color='blue'
-                                                title='See results'
-                                            />
-                                        )}
+                                        {
+                                            differentialExpressionAnalysis.state === DifferentialExpressionAnalysisExperimentState.COMPLETED && (
+                                                <Icon
+                                                    name='chart area'
+                                                    onClick={() => { openInferenceResult(differentialExpressionAnalysis) }}
+                                                    className='clickable'
+                                                    color='blue'
+                                                    title='See results'
+                                                />
+                                            )
+                                        }
                                         {/* Edit button */}
                                         <EditIcon
                                             editExperiment={() => handleEdit(differentialExpressionAnalysis)}
@@ -317,7 +315,7 @@ export const DiferentialExpressionPanel = () => {
                                                     }
 
                                                     {/* Delete button */}
-                                                    {!isInProcess && !differentialExpressionAnalysis.is_public && (
+                                                    {(!isInProcess && !differentialExpressionAnalysis.is_public) && (
                                                         <DeleteButton
                                                             title='Delete experiment'
                                                             onClick={() => confirmExperimentDeletion(differentialExpressionAnalysis)}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/types.ts b/src/frontend/static/frontend/src/components/differential-expression/types.ts
index 0b06e49d..4fef556b 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/types.ts
+++ b/src/frontend/static/frontend/src/components/differential-expression/types.ts
@@ -29,3 +29,15 @@ export interface DifferentialExpressionAnalysis {
     created_at: string;
     is_public: boolean;
 }
+
+export interface DiffExpExperimentDetail {
+    id: number;
+    gene: string;
+    ave_expr: number;
+    p_value: number;
+    adj_p_val: number;
+    log_fc: number;
+    t_statistic: number;
+    b_statistic: number;
+    is_significant: boolean;
+}
diff --git a/src/frontend/static/frontend/src/utils/util_functions.ts b/src/frontend/static/frontend/src/utils/util_functions.ts
index 6ef982fd..b46d4f1a 100644
--- a/src/frontend/static/frontend/src/utils/util_functions.ts
+++ b/src/frontend/static/frontend/src/utils/util_functions.ts
@@ -309,6 +309,14 @@ const getExperimentStateObjDiffExperiment = (state: DifferentialExpressionAnalys
                 title: 'The analysis has reached the timeout limit. Try changing some parameters and try again'
             }
             break
+        case DifferentialExpressionAnalysisExperimentState.NO_FEATURES_FOUND:
+            stateIconDiffExp = {
+                iconName: 'user outline',
+                color: 'red',
+                loading: false,
+                title: 'Datasets don\'t have samples in common'
+            }
+            break
         default:
             stateIconDiffExp = {
                 iconName: 'times',

From 80dc4688b95a55479e6e12506b01600393ba5099 Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Thu, 25 Dec 2025 20:42:27 -0300
Subject: [PATCH 31/47] Add volcano plot and results download endpoints

Introduces a new API endpoint to retrieve all differential expression results formatted for volcano plot visualization, and another endpoint to download all experiment results as a TSV file. Updates URL patterns to include these endpoints and implements permission checks to ensure only authorized users can access the data.
---
 src/differential_expression/urls.py  |  2 +
 src/differential_expression/views.py | 94 ++++++++++++++++++++++++++++
 2 files changed, 96 insertions(+)

diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index 1c4cd008..2ea51dc8 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -5,12 +5,14 @@
     path('', views.DifferentialExpressionList.as_view(), name='differential_expression_list'),
     path('results/', views.DifferentialExpressionDetail.as_view(), name='differential_expression_results'),
     path('results/<int:pk>/', views.DifferentialExpressionResults.as_view()),
+    path('volcano-data/<int:pk>/', views.DifferentialExpressionVolcanoData.as_view(), name='differential_expression_volcano_data'),
     path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
     path('stop-experiment', views.DifferentialExpressionStop.as_view(), name='differential_expression_stop'),
     path('update', views.DifferentialExpressionUpdate.as_view(), name='differential_expression_update'),
     path('update/<int:pk>/', views.DifferentialExpressionUpdate.as_view()),
     path('delete', views.DifferentialExpressionDelete.as_view(), name='differential_expression_delete'),
     path('delete/<int:pk>/', views.DifferentialExpressionDelete.as_view()),
+    path('download-results/<int:pk>/', views.download_differential_expression_results, name='download_differential_expression_results'),
     path('get-common-samples-differential-experiment', views.GetCommonSamplesDifferentialExperiment.as_view(), name='get_common_samples_differential_experiment'),
     path('get-common-samples-one-front-differential-experiment', views.GetCommonSamplesDifferentialOneFrontExperiment.as_view(), name='get_common_samples_one_front_differential_experiment'),
     path('switch-institution-public-view', views.ToggleDiffExperimentPublicView.as_view(), name='switch-diff-experiment-public-view'),
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 816c55d0..28a80c50 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -2,9 +2,13 @@
 from typing import Optional, Dict, Tuple, List
 
 import numpy as np
+import pandas as pd
 from celery.contrib.abortable import AbortableAsyncResult
+from django.contrib.auth.decorators import login_required
+from django.core.files.base import ContentFile
 from django.db import transaction
 from django.db.models import Q
+from django.http import HttpResponse
 from django_filters.rest_framework import DjangoFilterBackend
 from rest_framework import filters, generics, permissions, status
 from rest_framework.exceptions import ValidationError
@@ -313,6 +317,49 @@ def get_queryset(self):
         return experiment.results.all()
 
 
+class DifferentialExpressionVolcanoData(APIView):
+    """
+    Endpoint to get all results for a volcano plot visualization.
+    Returns all results without pagination in a format suitable for volcano plots.
+    """
+    permission_classes = [permissions.IsAuthenticated]
+
+    @staticmethod
+    def get(request: Request, pk: int):
+        """
+        Returns all experiment results formatted for volcano plot.
+        Returns: List of {id, label, log2FC, pValue}
+        """
+        experiment = get_object_or_404(DifferentialExpressionExperiment, pk=pk)
+
+        # Check permissions
+        user = request.user
+        if not (experiment.is_public or
+                experiment.user == user or
+                experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
+                experiment.shared_users.filter(id=user.id).exists()):
+            return Response(
+                {'error': 'You do not have permission to access this experiment.'},
+                status=status.HTTP_403_FORBIDDEN
+            )
+
+        # Get all results (no pagination)
+        results = experiment.results.all()
+
+        # Format data for volcano plot
+        volcano_data = [
+            {
+                'id': str(result.id),
+                'label': result.gene,
+                'log2FC': result.log_fc,
+                'pValue': result.adj_p_val
+            }
+            for result in results
+        ]
+
+        return Response(volcano_data)
+
+
 class DifferentialExpressionStop(APIView):
     """
     Endpoint to stop a differential expression experiment.
@@ -687,3 +734,50 @@ def get_samples_list(
             }
 
     return list_of_samples, response
+
+
+@login_required
+def download_differential_expression_results(request, pk: int):
+    """
+    Downloads all the differential expression results for a specific experiment.
+    Returns a TSV file with all results (no pagination).
+    """
+    experiment = get_object_or_404(DifferentialExpressionExperiment, pk=pk)
+
+    # Check permissions
+    user = request.user
+    if not (experiment.is_public or
+            experiment.user == user or
+            experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
+            experiment.shared_users.filter(id=user.id).exists()):
+        return HttpResponse('Unauthorized', status=401)
+
+    # Get all results (no pagination)
+    results = experiment.results.all().order_by('adj_p_val')
+
+    if not results.exists():
+        return HttpResponse('No results found for this experiment', status=404)
+
+    # Convert results to list of dictionaries
+    results_data = []
+    for result in results:
+        results_data.append({
+            'gene': result.gene,
+            'log_fc': result.log_fc,
+            'ave_expr': result.ave_expr,
+            't_statistic': result.t_statistic,
+            'p_value': result.p_value,
+            'adj_p_val': result.adj_p_val,
+            'b_statistic': result.b_statistic
+        })
+
+    # Create DataFrame and convert to TSV
+    df = pd.DataFrame(results_data)
+    file_to_send = ContentFile(df.to_csv(sep='\t', decimal='.', index=False))
+
+    # Generate HTTP response for file download
+    response = HttpResponse(file_to_send, 'text/csv')
+    response['Content-Length'] = file_to_send.size
+    response['Content-Disposition'] = f'attachment; filename="{experiment.name}_results.tsv"'
+
+    return response

From 72ebfafb649bb9075d0c615c9059b89122ca8f2d Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Thu, 25 Dec 2025 20:49:03 -0300
Subject: [PATCH 32/47] Add volcano plot serializer and refactor volcano data
 endpoint

Introduced DifferentialExpressionVolcanoPlotSerializer for minimal volcano plot data. Refactored DifferentialExpressionVolcanoData view to use ListAPIView, leverage the new serializer, and remove manual response formatting and permission handling.
---
 src/differential_expression/serializers.py | 14 ++++++++
 src/differential_expression/views.py       | 39 +++++++---------------
 2 files changed, 26 insertions(+), 27 deletions(-)

diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index 691c8aa9..533fe9e1 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -44,6 +44,20 @@ def get_is_significant(obj):
         return obj.adj_p_val <= 0.05 and abs(obj.log_fc) >= 1.0
 
 
+class DifferentialExpressionVolcanoPlotSerializer(serializers.ModelSerializer):
+    """
+    Serializer for volcano plot visualization.
+    Returns minimal fields needed for plotting: id, label (gene name), log2FC, and pValue (adj.P.Val).
+    """
+    label = serializers.CharField(source='gene', read_only=True)
+    log2FC = serializers.FloatField(source='log_fc', read_only=True)
+    pValue = serializers.FloatField(source='adj_p_val', read_only=True)
+
+    class Meta:
+        model = DifferentialExpressionExperimentResult
+        fields = ['id', 'label', 'log2FC', 'pValue']
+
+
 class DifferentialExpressionExperimentListSerializer(serializers.ModelSerializer):
     """
     Optimized serializer for differential expression experiments list view.
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 28a80c50..8fbcec59 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -35,6 +35,7 @@
     DifferentialExpressionExperimentDetailSerializer,
     DifferentialExpressionExperimentResultSerializer,
     DifferentialExpressionExperimentListSerializer,
+    DifferentialExpressionVolcanoPlotSerializer,
 )
 from user_files.models import UserFile
 from user_files.models_choices import FileType
@@ -317,47 +318,31 @@ def get_queryset(self):
         return experiment.results.all()
 
 
-class DifferentialExpressionVolcanoData(APIView):
+class DifferentialExpressionVolcanoData(generics.ListAPIView):
     """
     Endpoint to get all results for a volcano plot visualization.
     Returns all results without pagination in a format suitable for volcano plots.
+    Format: [{id, label, log2FC, pValue}, ...]
     """
+    serializer_class = DifferentialExpressionVolcanoPlotSerializer
     permission_classes = [permissions.IsAuthenticated]
+    pagination_class = None  # Disable pagination for volcano plot
 
-    @staticmethod
-    def get(request: Request, pk: int):
-        """
-        Returns all experiment results formatted for volcano plot.
-        Returns: List of {id, label, log2FC, pValue}
-        """
+    def get_queryset(self):
+        """Get all results for the specified experiment with permission checks."""
+        pk = self.kwargs.get('pk')
         experiment = get_object_or_404(DifferentialExpressionExperiment, pk=pk)
 
         # Check permissions
-        user = request.user
+        user = self.request.user
         if not (experiment.is_public or
                 experiment.user == user or
                 experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
                 experiment.shared_users.filter(id=user.id).exists()):
-            return Response(
-                {'error': 'You do not have permission to access this experiment.'},
-                status=status.HTTP_403_FORBIDDEN
-            )
-
-        # Get all results (no pagination)
-        results = experiment.results.all()
-
-        # Format data for volcano plot
-        volcano_data = [
-            {
-                'id': str(result.id),
-                'label': result.gene,
-                'log2FC': result.log_fc,
-                'pValue': result.adj_p_val
-            }
-            for result in results
-        ]
+            raise ValidationError('You do not have permission to access this experiment.')
 
-        return Response(volcano_data)
+        # Return all results (no pagination)
+        return experiment.results.all()
 
 
 class DifferentialExpressionStop(APIView):

From 5bbc3785d15ceb6caf6c7e495bfab6cc04959a53 Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Mon, 5 Jan 2026 03:54:26 -0300
Subject: [PATCH 33/47] Differential expression detail

Add results table of experiment.
Add Volcano plot and csv donwload
---
 src/differential_expression/urls.py           |    6 +-
 src/differential_expression/views.py          |    2 +-
 .../static/frontend/package-lock.json         | 2160 ++++++++++++++++-
 src/frontend/static/frontend/package.json     |   11 +-
 .../DifferentialExpressionModalResults.tsx    |  105 +-
 ...rentialExpressionModalResultsTableView.tsx |   87 +
 ...ntialExpressionModalResultsVolcanoPlot.tsx |   97 +
 .../DifferentialExpressionPanel.tsx           |    8 +-
 .../differential-expression/VolcanoPlot.tsx   |   98 +
 .../differential-expression/types.ts          |    8 +
 .../src/css/differential-expression.css       |    5 +-
 .../frontend/differential-expression.html     |    2 +
 12 files changed, 2372 insertions(+), 217 deletions(-)
 create mode 100644 src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsTableView.tsx
 create mode 100644 src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
 create mode 100644 src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx

diff --git a/src/differential_expression/urls.py b/src/differential_expression/urls.py
index 2ea51dc8..19c38e54 100644
--- a/src/differential_expression/urls.py
+++ b/src/differential_expression/urls.py
@@ -5,14 +5,16 @@
     path('', views.DifferentialExpressionList.as_view(), name='differential_expression_list'),
     path('results/', views.DifferentialExpressionDetail.as_view(), name='differential_expression_results'),
     path('results/<int:pk>/', views.DifferentialExpressionResults.as_view()),
-    path('volcano-data/<int:pk>/', views.DifferentialExpressionVolcanoData.as_view(), name='differential_expression_volcano_data'),
+    path('volcano-data', views.DifferentialExpressionVolcanoData.as_view(), name='differential_expression_volcano_data'),
+    path('volcano-data/<int:pk>/', views.DifferentialExpressionVolcanoData.as_view()),
     path('submit-experiment', views.DifferentialExpressionSubmit.as_view(), name='differential_expression_submit'),
     path('stop-experiment', views.DifferentialExpressionStop.as_view(), name='differential_expression_stop'),
     path('update', views.DifferentialExpressionUpdate.as_view(), name='differential_expression_update'),
     path('update/<int:pk>/', views.DifferentialExpressionUpdate.as_view()),
     path('delete', views.DifferentialExpressionDelete.as_view(), name='differential_expression_delete'),
     path('delete/<int:pk>/', views.DifferentialExpressionDelete.as_view()),
-    path('download-results/<int:pk>/', views.download_differential_expression_results, name='download_differential_expression_results'),
+    path('download-results', views.download_differential_expression_results, name='download_differential_expression_results'),
+    path('download-results/<int:pk>/', views.download_differential_expression_results),
     path('get-common-samples-differential-experiment', views.GetCommonSamplesDifferentialExperiment.as_view(), name='get_common_samples_differential_experiment'),
     path('get-common-samples-one-front-differential-experiment', views.GetCommonSamplesDifferentialOneFrontExperiment.as_view(), name='get_common_samples_one_front_differential_experiment'),
     path('switch-institution-public-view', views.ToggleDiffExperimentPublicView.as_view(), name='switch-diff-experiment-public-view'),
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 8fbcec59..c951b8b8 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -163,7 +163,7 @@ def get_queryset(self):
     pagination_class = StandardResultsSetPagination
     filter_backends = [filters.OrderingFilter, filters.SearchFilter, DjangoFilterBackend]
     search_fields = ['name', 'description']
-    filterset_fields = ['tool', ]
+    filterset_fields = ['tool']
 
 
 class DifferentialExpressionSubmit(APIView):
diff --git a/src/frontend/static/frontend/package-lock.json b/src/frontend/static/frontend/package-lock.json
index e5b30b61..b6e3a75c 100644
--- a/src/frontend/static/frontend/package-lock.json
+++ b/src/frontend/static/frontend/package-lock.json
@@ -23,11 +23,13 @@
         "ky": "^1.7.5",
         "lodash": "^4.17.21",
         "neo-react-semantic-ui-range": "^0.3.6",
+        "plotly.js": "^3.3.0",
         "react": "^18.3.1",
         "react-apexcharts": "^1.4.1",
         "react-avatar": "^5.0.3",
         "react-colorful": "^5.6.1",
         "react-dom": "^18.3.1",
+        "react-plotly.js": "^2.6.0",
         "react-virtualized": "^9.22.6",
         "recharts": "^2.15.1",
         "semantic-ui-react": "^2.1.5",
@@ -2178,6 +2180,24 @@
       "resolved": "https://registry.npmjs.org/@bcoe/v8-coverage/-/v8-coverage-0.2.3.tgz",
       "integrity": "sha512-0hYQ8SB4Db5zvZB4axdMHGwEaQjkZzFjQiN9LVYvIFB2nSUHW9tYpxWriPrWDASIxiaXax83REcLxuSdnGPZtw=="
     },
+    "node_modules/@choojs/findup": {
+      "version": "0.2.1",
+      "resolved": "https://registry.npmjs.org/@choojs/findup/-/findup-0.2.1.tgz",
+      "integrity": "sha512-YstAqNb0MCN8PjdLCDfRsBcGVRN41f3vgLvaI0IrIcBp4AqILRSS0DeWNGkicC+f/zRIPJLc+9RURVSepwvfBw==",
+      "license": "MIT",
+      "dependencies": {
+        "commander": "^2.15.1"
+      },
+      "bin": {
+        "findup": "bin/findup.js"
+      }
+    },
+    "node_modules/@choojs/findup/node_modules/commander": {
+      "version": "2.20.3",
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-    "node_modules/type-check": {
-      "version": "0.3.2",
-      "resolved": "https://registry.npmjs.org/type-check/-/type-check-0.3.2.tgz",
-      "integrity": "sha512-ZCmOJdvOWDBYJlzAoFkC+Q0+bUyEOS1ltgp1MGU03fqHG+dbi9tBFU2Rd9QKiDZFAYrhPh2JUf7rZRIuHRKtOg==",
-      "dependencies": {
-        "prelude-ls": "~1.1.2"
-      },
-      "engines": {
-        "node": ">= 0.8.0"
-      }
-    },
     "node_modules/type-detect": {
       "version": "4.0.8",
       "resolved": "https://registry.npmjs.org/type-detect/-/type-detect-4.0.8.tgz",
@@ -27255,6 +29118,16 @@
       "resolved": "https://registry.npmjs.org/typedarray/-/typedarray-0.0.6.tgz",
       "integrity": "sha512-/aCDEGatGvZ2BIk+HmLf4ifCJFwvKFNb9/JeZPMulfgFracn9QFcAf5GO8B/mweUjSoblS5In0cWhqpfs/5PQA=="
     },
+    "node_modules/typedarray-pool": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/typedarray-pool/-/typedarray-pool-1.2.0.tgz",
+      "integrity": "sha512-YTSQbzX43yvtpfRtIDAYygoYtgT+Rpjuxy9iOpczrjpXLgGoyG7aS5USJXV2d3nn8uHTeb9rXDvzS27zUg5KYQ==",
+      "license": "MIT",
+      "dependencies": {
+        "bit-twiddle": "^1.0.0",
+        "dup": "^1.0.0"
+      }
+    },
     "node_modules/typedarray-to-buffer": {
       "version": "3.1.5",
       "resolved": "https://registry.npmjs.org/typedarray-to-buffer/-/typedarray-to-buffer-3.1.5.tgz",
@@ -27555,6 +29428,12 @@
       "resolved": "https://registry.npmjs.org/picocolors/-/picocolors-1.1.1.tgz",
       "integrity": "sha512-xceH2snhtb5M9liqDsmEw56le376mTZkEX/jEb/RxNFyegNul7eNslCXP9FDj/Lcu0X8KEyMceP2ntpaHrDEVA=="
     },
+    "node_modules/update-diff": {
+      "version": "1.1.0",
+      "resolved": "https://registry.npmjs.org/update-diff/-/update-diff-1.1.0.tgz",
+      "integrity": "sha512-rCiBPiHxZwT4+sBhEbChzpO5hYHjm91kScWgdHf4Qeafs6Ba7MBl+d9GlGv72bcTZQO0sLmtQS1pHSWoCLtN/A==",
+      "license": "MIT"
+    },
     "node_modules/uri-js": {
       "version": "4.4.1",
       "resolved": "https://registry.npmjs.org/uri-js/-/uri-js-4.4.1.tgz",
@@ -27860,6 +29739,17 @@
       "resolved": "https://registry.npmjs.org/vm-browserify/-/vm-browserify-1.1.2.tgz",
       "integrity": "sha512-2ham8XPWTONajOR0ohOKOHXkm3+gaBmGut3SRuu75xLd/RRaY6vqgh8NBYYk7+RW3u5AtzPQZG8F10LHkl0lAQ=="
     },
+    "node_modules/vt-pbf": {
+      "version": "3.1.3",
+      "resolved": "https://registry.npmjs.org/vt-pbf/-/vt-pbf-3.1.3.tgz",
+      "integrity": "sha512-2LzDFzt0mZKZ9IpVF2r69G9bXaP2Q2sArJCmcCgvfTdCCZzSyz4aCLoQyUilu37Ll56tCblIZrXFIjNUpGIlmA==",
+      "license": "MIT",
+      "dependencies": {
+        "@mapbox/point-geometry": "0.1.0",
+        "@mapbox/vector-tile": "^1.3.1",
+        "pbf": "^3.2.1"
+      }
+    },
     "node_modules/w3c-hr-time": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/w3c-hr-time/-/w3c-hr-time-1.0.2.tgz",
@@ -28167,6 +30057,21 @@
         "minimalistic-assert": "^1.0.0"
       }
     },
+    "node_modules/weak-map": {
+      "version": "1.0.8",
+      "resolved": "https://registry.npmjs.org/weak-map/-/weak-map-1.0.8.tgz",
+      "integrity": "sha512-lNR9aAefbGPpHO7AEnY0hCFjz1eTkWCXYvkTRrTHs9qv8zJp+SkVYpzfLIFXQQiG3tVvbNFQgVg2bQS8YGgxyw==",
+      "license": "Apache-2.0"
+    },
+    "node_modules/webgl-context": {
+      "version": "2.2.0",
+      "resolved": "https://registry.npmjs.org/webgl-context/-/webgl-context-2.2.0.tgz",
+      "integrity": "sha512-q/fGIivtqTT7PEoF07axFIlHNk/XCPaYpq64btnepopSWvKNFkoORlQYgqDigBIuGA1ExnFd/GnSUnBNEPQY7Q==",
+      "license": "MIT",
+      "dependencies": {
+        "get-canvas-context": "^1.0.1"
+      }
+    },
     "node_modules/webidl-conversions": {
       "version": "6.1.0",
       "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-6.1.0.tgz",
@@ -29667,6 +31572,15 @@
         "microevent.ts": "~0.1.1"
       }
     },
+    "node_modules/world-calendars": {
+      "version": "1.0.4",
+      "resolved": "https://registry.npmjs.org/world-calendars/-/world-calendars-1.0.4.tgz",
+      "integrity": "sha512-VGRnLJS+xJmGDPodgJRnGIDwGu0s+Cr9V2HB3EzlDZ5n0qb8h5SJtGUEkjrphZYAglEiXZ6kiXdmk0H/h/uu/w==",
+      "license": "MIT",
+      "dependencies": {
+        "object-assign": "^4.1.0"
+      }
+    },
     "node_modules/wrap-ansi": {
       "version": "6.2.0",
       "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-6.2.0.tgz",
diff --git a/src/frontend/static/frontend/package.json b/src/frontend/static/frontend/package.json
index b3c8a873..fd73478c 100644
--- a/src/frontend/static/frontend/package.json
+++ b/src/frontend/static/frontend/package.json
@@ -22,11 +22,6 @@
     "@babel/preset-env": "^7.27.2",
     "@babel/preset-react": "^7.27.1",
     "@babel/preset-typescript": "^7.27.1",
-    "babel-loader": "^10.0.0",
-    "babel-plugin-react-compiler": "^19.1.0-rc.2",
-    "eslint-plugin-react-compiler": "^19.1.0-rc.2",
-    "react-compiler-runtime": "^19.1.0-rc.2",
-
     "@eslint/compat": "^1.2.8",
     "@eslint/eslintrc": "^3.3.1",
     "@eslint/js": "^9.27.0",
@@ -37,13 +32,17 @@
     "@types/react-dom": "^18.3.5",
     "@types/react-virtualized": "^9.22.2",
     "@types/validator": "^13.12.3",
+    "babel-loader": "^10.0.0",
+    "babel-plugin-react-compiler": "^19.1.0-rc.2",
     "css-loader": "^7.1.2",
     "eslint": "^9.27.0",
     "eslint-plugin-jsdoc": "^50.6.9",
     "eslint-plugin-react": "^7.37.4",
+    "eslint-plugin-react-compiler": "^19.1.0-rc.2",
     "eslint-plugin-react-hooks": "^5.2.0",
     "globals": "^16.0.0",
     "neostandard": "^0.12.1",
+    "react-compiler-runtime": "^19.1.0-rc.2",
     "style-loader": "^4.0.0",
     "ts-checker-rspack-plugin": "^1.1.1",
     "ts-loader": "^9.5.2",
@@ -67,11 +66,13 @@
     "ky": "^1.7.5",
     "lodash": "^4.17.21",
     "neo-react-semantic-ui-range": "^0.3.6",
+    "plotly.js": "^3.3.0",
     "react": "^18.3.1",
     "react-apexcharts": "^1.4.1",
     "react-avatar": "^5.0.3",
     "react-colorful": "^5.6.1",
     "react-dom": "^18.3.1",
+    "react-plotly.js": "^2.6.0",
     "react-virtualized": "^9.22.6",
     "recharts": "^2.15.1",
     "semantic-ui-react": "^2.1.5",
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
index 118633b3..4afe0923 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
@@ -1,10 +1,8 @@
-import React from 'react'
-import { DifferentialExpressionAnalysis, DiffExpExperimentDetail } from './types'
-import { Icon, Modal, Table, TableCell } from 'semantic-ui-react'
-import { TableCellWithTitle } from '../common/TableCellWithTitle'
-import { PaginatedTable } from '../common/PaginatedTable'
-
-declare const urlDifferentialExpressionExperimentResults: string
+import React, { useMemo } from 'react'
+import { DifferentialExpressionAnalysis } from './types'
+import { Icon, Modal, Tab, TabPane } from 'semantic-ui-react'
+import { DifferentialExpressionModalResultsTableView } from './DifferentialExpressionModalResultsTableView'
+import { DifferentialExpressionModalResultsVolcanoPlot } from './DifferentialExpressionModalResultsVolcanoPlot'
 
 interface DifferentialExpressionModalResultsProps {
     isOpen: boolean
@@ -13,6 +11,24 @@ interface DifferentialExpressionModalResultsProps {
 }
 
 export const DifferentialExpressionModalResults = (props: DifferentialExpressionModalResultsProps) => {
+    const panes = useMemo(() => [
+        {
+            menuItem: 'Table',
+            render: () => (
+                <TabPane>
+                    <DifferentialExpressionModalResultsTableView differentialExpressionAnalysisId={props.differentialExpressionAnalysis?.id as number} />
+                </TabPane>
+            )
+        },
+        {
+            menuItem: 'Volcano Plot',
+            render: () => (
+                <TabPane>
+                    <DifferentialExpressionModalResultsVolcanoPlot differentialExpressionAnalysisId={props.differentialExpressionAnalysis?.id as number} />
+                </TabPane>
+            )
+        },
+    ], [props.differentialExpressionAnalysis?.id])
     return (
         <Modal
             open={props.isOpen}
@@ -23,80 +39,7 @@ export const DifferentialExpressionModalResults = (props: DifferentialExpression
             className='space-modal large-modal'
             onClose={props.closeModal}
         >
-            <PaginatedTable<DiffExpExperimentDetail>
-                headerTitle='Differential Expressions experiment result'
-                headers={[
-                    { name: 'Gene', serverCodeToSort: 'gene' },
-                    { name: 'adj_p_val', serverCodeToSort: 'adj_p_val' },
-                    { name: 'ave_expr', serverCodeToSort: 'ave_expr' },
-                    { name: 'b_statistic', serverCodeToSort: 'b_statistic' },
-                    { name: 'log_fc', serverCodeToSort: 'log_fc' },
-                    { name: 'is_significant', serverCodeToSort: 'is_significant' },
-                    { name: 'p_value', serverCodeToSort: 'p_value' },
-                    { name: 't_statistic', serverCodeToSort: 't_statistic' },
-
-                ]}
-                defaultSortProp={{ sortField: 'created_at', sortOrderAscendant: false }}
-                customFilters={undefined}
-                showSearchInput
-                customElements={[
-                    /*  <Form.Field key={1} className='custom-table-field' title='Add new Biomarker'>
-                        <Button
-                            primary
-                            icon
-                            onClick={() => this.setState({ formBiomarker: this.getDefaultFormBiomarker(), openCreateEditBiomarkerModal: true })}
-                        >
-                            <Icon name='add' />
-                        </Button>
-                    </Form.Field> */
-                ]}
-                searchLabel='Gene'
-                searchPlaceholder='Search by Gene'
-                urlToRetrieveData={urlDifferentialExpressionExperimentResults + props.differentialExpressionAnalysis?.id + '/'}
-                updateWSKey='update_differential_expression_experiments'
-                mapFunction={(differentialExpressionAnalysis: DiffExpExperimentDetail) => {
-                    return (
-                        <Table.Row key={differentialExpressionAnalysis.id as number}>
-                            <TableCellWithTitle value={differentialExpressionAnalysis.gene} />
-                            <TableCellWithTitle value={differentialExpressionAnalysis.adj_p_val.toString()} />
-                            <TableCell>
-                                {differentialExpressionAnalysis.ave_expr}
-                            </TableCell>
-                            <TableCell>
-                                {differentialExpressionAnalysis.b_statistic}
-                            </TableCell>
-                            <TableCell>
-                                {differentialExpressionAnalysis.log_fc}
-                            </TableCell>
-                            <TableCell textAlign='center'>
-                                {
-                                    differentialExpressionAnalysis.is_significant
-                                        ? (
-                                            <Icon
-                                                title='Is significant'
-                                                name='check'
-                                                color='green'
-                                            />
-                                        )
-                                        : (
-                                            <Icon
-                                                title='Is not significant'
-                                                name='close'
-                                                color='red'
-                                            />
-                                        )
-                                }
-                            </TableCell>
-                            <TableCell>
-                                {differentialExpressionAnalysis.p_value}
-                            </TableCell>
-                            <TableCell>
-                                {differentialExpressionAnalysis.t_statistic}
-                            </TableCell>
-                        </Table.Row>
-                    )
-                }}
-            />
+            <Tab panes={panes} />
         </Modal>
     )
 }
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsTableView.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsTableView.tsx
new file mode 100644
index 00000000..9e90674c
--- /dev/null
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsTableView.tsx
@@ -0,0 +1,87 @@
+import React, { useMemo } from 'react'
+import { Table, Icon, TableCell, Form, Button } from 'semantic-ui-react'
+import { PaginatedTable } from '../common/PaginatedTable'
+import { DiffExpExperimentDetail } from './types'
+import { TableCellWithTitle } from '../common/TableCellWithTitle'
+declare const urlDifferentialExpressionExperimentResults: string
+declare const urlDownloadDifferentialExpressionResults: string
+
+interface DifferentialExpressionModalResultsProps {
+    differentialExpressionAnalysisId?: number;
+}
+
+export const DifferentialExpressionModalResultsTableView = (props: DifferentialExpressionModalResultsProps) => {
+    const downloadUrl = useMemo(() => {
+        const searchParams = new URLSearchParams()
+
+        return `${urlDownloadDifferentialExpressionResults}/${props.differentialExpressionAnalysisId}?${searchParams.toString()}`
+    }, [props.differentialExpressionAnalysisId])
+
+    const onDownload = () => {
+        window.open(downloadUrl, '_blank', 'noopener,noreferrer')
+    }
+
+    return (
+        <>
+            <PaginatedTable<DiffExpExperimentDetail>
+                headerTitle='Differential Expressions experiment result'
+                headers={[
+                    { name: 'Gene', serverCodeToSort: 'gene' },
+                    { name: 'adj_p_val', serverCodeToSort: 'adj_p_val' },
+                    { name: 'ave_expr', serverCodeToSort: 'ave_expr' },
+                    { name: 'b_statistic', serverCodeToSort: 'b_statistic' },
+                    { name: 'log_fc', serverCodeToSort: 'log_fc' },
+                    { name: 'is_significant', serverCodeToSort: 'is_significant' },
+                    { name: 'p_value', serverCodeToSort: 'p_value' },
+                    { name: 't_statistic', serverCodeToSort: 't_statistic' },
+                ]}
+                defaultSortProp={{ sortField: 'created_at', sortOrderAscendant: false }}
+                customFilters={undefined}
+                showSearchInput
+                customElements={[
+                    <Form.Field key='download-csv-button' className='custom-table-field' title='Download results in a CSV file'>
+                        <Button
+                            color='green'
+                            icon
+                            type='button'
+                            onClick={onDownload}
+                            title='Download results in a CSV file'
+                        >
+                            <Icon name='file excel' />
+                        </Button>
+                    </Form.Field>
+                ]}
+                searchLabel='Gene'
+                searchPlaceholder='Search by Gene'
+                urlToRetrieveData={urlDifferentialExpressionExperimentResults + props.differentialExpressionAnalysisId + '/'}
+                updateWSKey='update_differential_expression_experiments'
+                mapFunction={(differentialExpressionAnalysis: DiffExpExperimentDetail) => (
+                    <Table.Row key={differentialExpressionAnalysis.id as number}>
+                        <TableCellWithTitle value={differentialExpressionAnalysis.gene} />
+                        <TableCellWithTitle
+                            value={differentialExpressionAnalysis.adj_p_val.toString()}
+                        />
+                        <TableCell>{differentialExpressionAnalysis.ave_expr}</TableCell>
+                        <TableCell>
+                            {differentialExpressionAnalysis.b_statistic}
+                        </TableCell>
+                        <TableCell>{differentialExpressionAnalysis.log_fc}</TableCell>
+                        <TableCell textAlign='center'>
+                            {differentialExpressionAnalysis.is_significant
+                                ? (
+                                    <Icon title='Is significant' name='check' color='green' />
+                                )
+                                : (
+                                    <Icon title='Is not significant' name='close' color='red' />
+                                )}
+                        </TableCell>
+                        <TableCell>{differentialExpressionAnalysis.p_value}</TableCell>
+                        <TableCell>
+                            {differentialExpressionAnalysis.t_statistic}
+                        </TableCell>
+                    </Table.Row>
+                )}
+            />
+        </>
+    )
+}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
new file mode 100644
index 00000000..c69e7c47
--- /dev/null
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
@@ -0,0 +1,97 @@
+import React, { useEffect, useState } from 'react'
+import VolcanoPlot from './VolcanoPlot'
+import ky from 'ky'
+import { VolcanoPoint } from './types'
+import { Form } from 'semantic-ui-react'
+
+declare const urlDifferentialExpressionVolcanoData: string
+
+interface DifferentialExpressionModalResultsVolcanoPlotProps {
+    differentialExpressionAnalysisId?: number;
+}
+
+export const DifferentialExpressionModalResultsVolcanoPlot = (props: DifferentialExpressionModalResultsVolcanoPlotProps) => {
+    const [volcanoPoints, setVolcanoPoints] = useState<VolcanoPoint[]>([])
+    const [fcThreshold, setFcThreshold] = useState<number>(1)
+    const [pThreshold, setPThreshold] = useState<number>(0.05)
+
+    const getVolcanoPlotData = (signal: AbortSignal) => {
+        if (!props.differentialExpressionAnalysisId) {
+            return
+        }
+
+        const url =
+            `${urlDifferentialExpressionVolcanoData}/` +
+            `${props.differentialExpressionAnalysisId}/`
+
+        ky.get(url, { retry: 5, signal }).then((response) => {
+            response.json().then((volcanoPointsResponse: VolcanoPoint[]) => {
+                setVolcanoPoints(volcanoPointsResponse)
+            }).catch((err) => {
+                console.error('Error parsing JSON ->', err)
+            })
+        }).catch((err) => {
+            console.error('Error getting volcanoPoints ->', err)
+        })
+    }
+
+    useEffect(() => {
+        const id = props.differentialExpressionAnalysisId
+
+        if (!id) {
+            return
+        }
+
+        const controller = new AbortController()
+        getVolcanoPlotData(controller.signal)
+
+        return () => {
+            controller.abort()
+        }
+    }, [
+        props.differentialExpressionAnalysisId
+    ])
+
+    return (
+        <div style={{ padding: 20 }}>
+            <h3>Volcano Plot</h3>
+
+            {/* 🔽 Selects */}
+            <Form>
+                <Form.Group widths='equal'>
+                    <Form.Select
+                        label='|log2FC| threshold'
+                        options={[
+                            { key: 1, text: '1', value: 1 },
+                            { key: 2, text: '2', value: 2 },
+                            { key: 3, text: '3', value: 3 },
+                        ]}
+                        value={fcThreshold}
+                        onChange={(_, data) =>
+                            setFcThreshold(Number(data.value))}
+                    />
+
+                    <Form.Select
+                        label='p-value threshold'
+                        options={[
+                            { key: 0.05, text: '0.05', value: 0.05 },
+                            { key: 0.01, text: '0.01', value: 0.01 },
+                        ]}
+                        value={pThreshold}
+                        onChange={(_, data) =>
+                            setPThreshold(Number(data.value))}
+                    />
+                </Form.Group>
+            </Form>
+
+            {/* 📊 Plot */}
+            {volcanoPoints.length > 0 && (
+                <VolcanoPlot
+                    data={volcanoPoints}
+                    fcThreshold={fcThreshold}
+                    pThreshold={pThreshold}
+                />
+            )}
+        </div>
+    )
+}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index aa70ea7c..1a56dd91 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -89,7 +89,7 @@ export const DiferentialExpressionPanel = () => {
         methodsOptions.unshift({ key: 'no_method', text: 'No method' })
 
         return [
-            { label: 'Method', keyForServer: 'method', defaultValue: '', placeholder: 'Select an existing method', options: methodsOptions, width: 3 }
+            { label: 'Method', keyForServer: 'tool', defaultValue: '', placeholder: 'Select an existing method', options: methodsOptions, width: 3 }
         ]
     }
 
@@ -197,8 +197,9 @@ export const DiferentialExpressionPanel = () => {
                     <PaginatedTable<DifferentialExpressionAnalysis>
                         headerTitle='Differential Expressions Analyses'
                         headers={[
-                            { name: 'Name', serverCodeToSort: 'name', width: 3 },
-                            { name: 'Description', serverCodeToSort: 'description', width: 4 },
+                            { name: 'Name', serverCodeToSort: 'name', width: 2 },
+                            { name: 'Description', serverCodeToSort: 'description', width: 3 },
+                            { name: 'Method', serverCodeToSort: 'tool' },
                             { name: 'Date', serverCodeToSort: 'created_at' },
                             { name: 'State', serverCodeToSort: 'state', width: 1, textAlign: 'center' },
                             { name: 'Sources' },
@@ -232,6 +233,7 @@ export const DiferentialExpressionPanel = () => {
                                 <Table.Row key={differentialExpressionAnalysis.id as number}>
                                     <TableCellWithTitle value={differentialExpressionAnalysis.name} />
                                     <TableCellWithTitle value={differentialExpressionAnalysis.description} />
+                                    <TableCellWithTitle value={differentialExpressionAnalysis.tool} />
                                     <TableCellWithTitle value={formatDateLocale(differentialExpressionAnalysis.created_at as string, 'L')} />
                                     <TableCell textAlign='center'>
                                         <Icon
diff --git a/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
new file mode 100644
index 00000000..100676bf
--- /dev/null
+++ b/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
@@ -0,0 +1,98 @@
+import React from 'react'
+import Plot from 'react-plotly.js'
+
+type VolcanoPoint = {
+    id: string | number;
+    label?: string;
+    log2FC: number; // X axis
+    pValue: number;// it converts to Y axis -log10(pValue)
+}
+
+interface VolcanoPlotProps {
+    data: VolcanoPoint[];
+    fcThreshold?: number; // umbral of |log2FC|
+    pThreshold?: number; // umbral of p-value
+}
+
+const VolcanoPlot: React.FC<VolcanoPlotProps> = ({
+    data,
+    fcThreshold = 1, // default |log2FC| > 1
+    pThreshold = 0.05, // default p < 0.05
+}) => {
+    // Converts tp -log10(p)
+    const transformP = (p: number) => -Math.log10(p)
+
+    // Separate in 3 groups: up, down, no significativos
+    const upregulated = data.filter(
+        d => d.log2FC >= fcThreshold && d.pValue <= pThreshold
+    )
+    const downregulated = data.filter(
+        d => d.log2FC <= -fcThreshold && d.pValue <= pThreshold
+    )
+    const nonsignificant = data.filter(
+        d => !upregulated.includes(d) && !downregulated.includes(d)
+    )
+
+    return (
+        <Plot
+            data={[
+                {
+                    x: upregulated.map(d => d.log2FC),
+                    y: upregulated.map(d => transformP(d.pValue)),
+                    text: upregulated.map(d => d.label ?? d.id),
+                    mode: 'markers',
+                    type: 'scattergl',
+                    name: 'Up',
+                    marker: { size: 6 },
+                    hovertemplate:
+                    'log2FC: %{x:.2f}<br>-log10(p): %{y:.2f}<br>%{text}<extra></extra>',
+                },
+                {
+                    x: downregulated.map(d => d.log2FC),
+                    y: downregulated.map(d => transformP(d.pValue)),
+                    text: downregulated.map(d => d.label ?? d.id),
+                    mode: 'markers',
+                    type: 'scattergl',
+                    name: 'Down',
+                    marker: { size: 6 },
+                    hovertemplate:
+                        'log2FC: %{x:.2f}<br>-log10(p): %{y:.2f}<br>%{text}<extra></extra>',
+                },
+                {
+                    x: nonsignificant.map(d => d.log2FC),
+                    y: nonsignificant.map(d => transformP(d.pValue)),
+                    text: nonsignificant.map(d => d.label ?? d.id),
+                    mode: 'markers',
+                    type: 'scattergl',
+                    name: 'No sig.',
+                    marker: { size: 4, opacity: 0.6 },
+                    hovertemplate:
+                    'log2FC: %{x:.2f}<br>-log10(p): %{y:.2f}<br>%{text}<extra></extra>',
+                },
+            ]}
+            layout={{
+                title: 'Volcano plot',
+                xaxis: {
+                    title: 'log2(Fold Change)',
+                    zeroline: true,
+                    zerolinewidth: 1,
+                },
+                yaxis: {
+                    title: '-log10(p-value)',
+                    zeroline: false,
+                },
+                hovermode: 'closest',
+                showlegend: true,
+                margin: { l: 60, r: 20, t: 40, b: 50 },
+            }}
+            config={{
+                responsive: true,
+                displayModeBar: true,
+            }}
+            key={`${fcThreshold}-${pThreshold}`}
+            style={{ width: '100%', height: '500px' }}
+        />
+    )
+}
+
+export default VolcanoPlot
diff --git a/src/frontend/static/frontend/src/components/differential-expression/types.ts b/src/frontend/static/frontend/src/components/differential-expression/types.ts
index 4fef556b..0654df7c 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/types.ts
+++ b/src/frontend/static/frontend/src/components/differential-expression/types.ts
@@ -21,6 +21,7 @@ export interface DifferentialExpressionAnalysis {
     id: number;
     name: string;
     description: string;
+    tool: string;
     user: DjangoUser;
     clinical_source: DjangoExperimentSource;
     mrna_source: DjangoExperimentSource;
@@ -41,3 +42,10 @@ export interface DiffExpExperimentDetail {
     b_statistic: number;
     is_significant: boolean;
 }
+
+export type VolcanoPoint = {
+    id: string;
+    label: string;
+    log2FC: number;
+    pValue: number; // adj.P.Val
+}
diff --git a/src/frontend/static/frontend/src/css/differential-expression.css b/src/frontend/static/frontend/src/css/differential-expression.css
index bdda5ac3..b8c6d635 100644
--- a/src/frontend/static/frontend/src/css/differential-expression.css
+++ b/src/frontend/static/frontend/src/css/differential-expression.css
@@ -17,8 +17,9 @@
     margin-bottom: 10px;
 }
 .large-modal {
-    min-height: 92% !important;
-    width: 92% !important;
+    min-height: 76% !important;
+    width: 88% !important;
+    padding: 1rem !important;
 }
 
 .space-modal:nth-child(1) {
diff --git a/src/frontend/templates/frontend/differential-expression.html b/src/frontend/templates/frontend/differential-expression.html
index cca9898a..e27f367e 100644
--- a/src/frontend/templates/frontend/differential-expression.html
+++ b/src/frontend/templates/frontend/differential-expression.html
@@ -27,6 +27,8 @@
             const urlDeleteExperiment = "{% url 'differential_expression_delete' %}"
             const urlUpdateExperiment = "{% url 'differential_expression_update' %}"
             const urlDifferentialExpressionExperimentResults = "{% url 'differential_expression_results' %}"
+            const urlDownloadDifferentialExpressionResults = "{% url 'download_differential_expression_results' %}"
+            const urlDifferentialExpressionVolcanoData = "{% url 'differential_expression_volcano_data' %}"
         </script>
         {% render_bundle 'differentialExpression' 'js' %}
 {% endblock %}
\ No newline at end of file

From 0a55eab9a637b682101ec0a047c4c7b62ec8cc93 Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Thu, 8 Jan 2026 20:47:46 -0300
Subject: [PATCH 34/47] Update Dockerfiles and improve view error handling

Dockerfile and Dockerfile-celery comments were translated from Spanish to English for clarity. In views.py, replaced direct model get with get_object_or_404 for better error handling when retrieving CGDSStudy. Minor cleanup in admin.py by removing a redundant comment.
---
 Dockerfile                            | 4 ++--
 Dockerfile-celery                     | 4 ++--
 src/datasets_synchronization/views.py | 2 +-
 src/differential_expression/admin.py  | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 4cc64ce5..8d900f25 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -42,7 +42,7 @@ RUN apt-get update && apt-get install -y python3-pip curl libcurl4-openssl-dev l
     && curl -fsSL https://deb.nodesource.com/setup_20.x | bash - && apt-get install -y nodejs && mkdir /config \
     && mkdir /src
 
-# Instalar R 4.4.2 desde CRAN (Debian bookworm) y dependencias del sistema
+# Install R 4.4.2 from CRAN (Debian bookworm) and system dependencies
 RUN set -eux; \
   echo "deb http://deb.debian.org/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list; \
   printf 'APT::Default-Release "%s";\n' "bookworm" > /etc/apt/apt.conf.d/00default-release; \
@@ -56,7 +56,7 @@ RUN set -eux; \
     r-base=4.2.2.20221110-2 r-base-dev=4.2.2.20221110-2 r-recommended=4.2.2.20221110-2; \
   rm -rf /var/lib/apt/lists/*
 
-# Instalar Bioconductor limma (stats y base vienen con R)
+# Install Bioconductor limma (stats and base come with R)
 RUN R -q -e 'options(repos=c(CRAN="https://cloud.r-project.org")); install.packages("BiocManager"); BiocManager::install(version="3.16", ask=FALSE); BiocManager::install("limma", ask=FALSE, update=FALSE)'
 
 # Installs Python dependencies and compiles the frontend
diff --git a/Dockerfile-celery b/Dockerfile-celery
index a1822742..89b892b9 100644
--- a/Dockerfile-celery
+++ b/Dockerfile-celery
@@ -42,7 +42,7 @@ RUN apt-get update && apt-get install -y python3-pip curl libcurl4-openssl-dev l
     && mkdir /config \
     && mkdir /src
 
-# Instalar R 4.4.2 desde CRAN (Debian bookworm) y dependencias del sistema
+# Install R 4.4.2 from CRAN (Debian bookworm) and system dependencies
 RUN set -eux; \
   echo "deb http://deb.debian.org/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list; \
   printf 'APT::Default-Release "%s";\n' "bookworm" > /etc/apt/apt.conf.d/00default-release; \
@@ -56,7 +56,7 @@ RUN set -eux; \
     r-base=4.2.2.20221110-2 r-base-dev=4.2.2.20221110-2 r-recommended=4.2.2.20221110-2; \
   rm -rf /var/lib/apt/lists/*
 
-# Instalar Bioconductor limma (stats y base vienen con R)
+# Install Bioconductor limma (stats and base come with R)
 RUN R -q -e 'options(repos=c(CRAN="https://cloud.r-project.org")); install.packages("BiocManager"); BiocManager::install(version="3.16", ask=FALSE); BiocManager::install("limma", ask=FALSE, update=FALSE)'
 
 # Installs Python dependencies
diff --git a/src/datasets_synchronization/views.py b/src/datasets_synchronization/views.py
index 2836376a..e5ca5990 100644
--- a/src/datasets_synchronization/views.py
+++ b/src/datasets_synchronization/views.py
@@ -225,7 +225,7 @@ class CGDSDatasetClinicalAttributes(APIView):
     @staticmethod
     def get(request, pk: int):
         """Gets the clinical attributes of a CGDSDataset."""
-        cgds_study = CGDSStudy.objects.get(pk=pk)
+        cgds_study = get_object_or_404(CGDSStudy, pk=pk)
         # Gets the corresponding Study's Dataset
         cgds_dataset = get_cgds_dataset(cgds_study, FileType.CLINICAL)
         list_of_samples = cgds_dataset.get_column_names()
diff --git a/src/differential_expression/admin.py b/src/differential_expression/admin.py
index 2481d57d..4a170b85 100644
--- a/src/differential_expression/admin.py
+++ b/src/differential_expression/admin.py
@@ -182,7 +182,7 @@ def is_significant_display(self, obj):
     is_significant_display.boolean = True
 
 
-# Custom admin site configuration
+
 admin.site.site_header = "Multiomix Administration"
 admin.site.site_title = "Multiomix Admin"
 admin.site.index_title = "Welcome to Multiomix Administration"

From c7ad3faf409bba29a082188d0859eb425c8a26bd Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Wed, 14 Jan 2026 15:14:12 -0300
Subject: [PATCH 35/47] Fixs and update texts

---
 .../DifferentialExpressionModalResults.tsx    |  9 +-
 ...rentialExpressionModalResultsTableView.tsx | 10 +-
 ...ntialExpressionModalResultsVolcanoPlot.tsx |  4 +-
 .../differential-expression/VolcanoPlot.tsx   | 94 +++++++++----------
 4 files changed, 59 insertions(+), 58 deletions(-)

diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
index 4afe0923..89d11805 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
@@ -39,7 +39,14 @@ export const DifferentialExpressionModalResults = (props: DifferentialExpression
             className='space-modal large-modal'
             onClose={props.closeModal}
         >
-            <Tab panes={panes} />
+            <>
+                <Modal.Header>
+                    Differential Expression Analysis Results - {props.differentialExpressionAnalysis?.name}
+                </Modal.Header>
+                <Modal.Content scrolling>
+                    <Tab panes={panes} />
+                </Modal.Content>
+            </>
         </Modal>
     )
 }
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsTableView.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsTableView.tsx
index 9e90674c..884c3279 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsTableView.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsTableView.tsx
@@ -24,7 +24,7 @@ export const DifferentialExpressionModalResultsTableView = (props: DifferentialE
     return (
         <>
             <PaginatedTable<DiffExpExperimentDetail>
-                headerTitle='Differential Expressions experiment result'
+                headerTitle='Experiment results'
                 headers={[
                     { name: 'Gene', serverCodeToSort: 'gene' },
                     { name: 'adj_p_val', serverCodeToSort: 'adj_p_val' },
@@ -61,11 +61,11 @@ export const DifferentialExpressionModalResultsTableView = (props: DifferentialE
                         <TableCellWithTitle
                             value={differentialExpressionAnalysis.adj_p_val.toString()}
                         />
-                        <TableCell>{differentialExpressionAnalysis.ave_expr}</TableCell>
+                        <TableCell>{differentialExpressionAnalysis.ave_expr.toFixed(4)}</TableCell>
                         <TableCell>
-                            {differentialExpressionAnalysis.b_statistic}
+                            {differentialExpressionAnalysis.b_statistic.toFixed(4)}
                         </TableCell>
-                        <TableCell>{differentialExpressionAnalysis.log_fc}</TableCell>
+                        <TableCell>{differentialExpressionAnalysis.log_fc.toFixed(4)}</TableCell>
                         <TableCell textAlign='center'>
                             {differentialExpressionAnalysis.is_significant
                                 ? (
@@ -77,7 +77,7 @@ export const DifferentialExpressionModalResultsTableView = (props: DifferentialE
                         </TableCell>
                         <TableCell>{differentialExpressionAnalysis.p_value}</TableCell>
                         <TableCell>
-                            {differentialExpressionAnalysis.t_statistic}
+                            {differentialExpressionAnalysis.t_statistic.toFixed(4)}
                         </TableCell>
                     </Table.Row>
                 )}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
index c69e7c47..72461fa2 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
@@ -1,5 +1,5 @@
 import React, { useEffect, useState } from 'react'
-import VolcanoPlot from './VolcanoPlot'
+import { VolcanoPlot } from './VolcanoPlot'
 import ky from 'ky'
 import { VolcanoPoint } from './types'
 import { Form } from 'semantic-ui-react'
@@ -65,6 +65,8 @@ export const DifferentialExpressionModalResultsVolcanoPlot = (props: Differentia
                             { key: 1, text: '1', value: 1 },
                             { key: 2, text: '2', value: 2 },
                             { key: 3, text: '3', value: 3 },
+                            { key: 4, text: '4', value: 4 },
+                            { key: 5, text: '5', value: 5 }
                         ]}
                         value={fcThreshold}
                         onChange={(_, data) =>
diff --git a/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
index 100676bf..022fb8ed 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
@@ -2,97 +2,89 @@ import React from 'react'
 import Plot from 'react-plotly.js'
 
 type VolcanoPoint = {
-    id: string | number;
-    label?: string;
-    log2FC: number; // X axis
-    pValue: number;// it converts to Y axis -log10(pValue)
+    id: string | number
+    label?: string
+    log2FC: number // X axis
+    pValue: number // p-value (we plot -log10(p))
 }
 
 interface VolcanoPlotProps {
-    data: VolcanoPoint[];
-    fcThreshold?: number; // umbral of |log2FC|
-    pThreshold?: number; // umbral of p-value
+    data: VolcanoPoint[]
+    fcThreshold?: number
+    pThreshold?: number
 }
 
-const VolcanoPlot: React.FC<VolcanoPlotProps> = ({
+export const VolcanoPlot = ({
     data,
-    fcThreshold = 1, // default |log2FC| > 1
-    pThreshold = 0.05, // default p < 0.05
-}) => {
-    // Converts tp -log10(p)
+    fcThreshold = 1,
+    pThreshold = 0.05,
+}: VolcanoPlotProps) => {
     const transformP = (p: number) => -Math.log10(p)
 
-    // Separate in 3 groups: up, down, no significativos
-    const upregulated = data.filter(
-        d => d.log2FC >= fcThreshold && d.pValue <= pThreshold
-    )
-    const downregulated = data.filter(
-        d => d.log2FC <= -fcThreshold && d.pValue <= pThreshold
+    const significant = data.filter(
+        (d) => Math.abs(d.log2FC) >= fcThreshold && d.pValue <= pThreshold
     )
+
     const nonsignificant = data.filter(
-        d => !upregulated.includes(d) && !downregulated.includes(d)
+        (d) => !(Math.abs(d.log2FC) >= fcThreshold && d.pValue <= pThreshold)
     )
 
     return (
         <Plot
+            key={`${fcThreshold}-${pThreshold}`}
             data={[
                 {
-                    x: upregulated.map(d => d.log2FC),
-                    y: upregulated.map(d => transformP(d.pValue)),
-                    text: upregulated.map(d => d.label ?? d.id),
-                    mode: 'markers',
-                    type: 'scattergl',
-                    name: 'Up',
-                    marker: { size: 6 },
-                    hovertemplate:
-                    'log2FC: %{x:.2f}<br>-log10(p): %{y:.2f}<br>%{text}<extra></extra>',
-                },
-                {
-                    x: downregulated.map(d => d.log2FC),
-                    y: downregulated.map(d => transformP(d.pValue)),
-                    text: downregulated.map(d => d.label ?? d.id),
+                    x: significant.map((d) => d.log2FC),
+                    y: significant.map((d) => transformP(d.pValue)),
+                    text: significant.map((d) => d.label ?? d.id),
                     mode: 'markers',
                     type: 'scattergl',
-                    name: 'Down',
+                    name: 'Significant',
                     marker: { size: 6 },
                     hovertemplate:
-                        'log2FC: %{x:.2f}<br>-log10(p): %{y:.2f}<br>%{text}<extra></extra>',
+            '<b>Significant</b><br>' +
+            'log2FC: %{x:.2f}<br>' +
+            '-log10(p): %{y:.2f}<br>' +
+            '%{text}' +
+            '<extra></extra>',
                 },
                 {
-                    x: nonsignificant.map(d => d.log2FC),
-                    y: nonsignificant.map(d => transformP(d.pValue)),
-                    text: nonsignificant.map(d => d.label ?? d.id),
+                    x: nonsignificant.map((d) => d.log2FC),
+                    y: nonsignificant.map((d) => transformP(d.pValue)),
+                    text: nonsignificant.map((d) => d.label ?? d.id),
                     mode: 'markers',
                     type: 'scattergl',
-                    name: 'No sig.',
+                    name: 'Not significant',
                     marker: { size: 4, opacity: 0.6 },
                     hovertemplate:
-                    'log2FC: %{x:.2f}<br>-log10(p): %{y:.2f}<br>%{text}<extra></extra>',
+            '<b>Not significant</b><br>' +
+            'log2FC: %{x:.2f}<br>' +
+            '-log10(p): %{y:.2f}<br>' +
+            '%{text}' +
+            '<extra></extra>',
                 },
             ]}
             layout={{
-                title: 'Volcano plot',
+                title: 'Volcano Plot',
+                hovermode: 'closest',
+                showlegend: true,
+                margin: { l: 90, r: 40, t: 50, b: 70 },
+
+                // Axis labels (normal, not floating)
                 xaxis: {
-                    title: 'log2(Fold Change)',
-                    zeroline: true,
-                    zerolinewidth: 1,
+                    title: { text: 'log2(Fold Change)', standoff: 20 },
+                    zeroline: false,
                 },
                 yaxis: {
-                    title: '-log10(p-value)',
+                    title: { text: '-log10(p-value)', standoff: 10 },
                     zeroline: false,
                 },
-                hovermode: 'closest',
-                showlegend: true,
-                margin: { l: 60, r: 20, t: 40, b: 50 },
             }}
             config={{
                 responsive: true,
                 displayModeBar: true,
             }}
-            key={`${fcThreshold}-${pThreshold}`}
             style={{ width: '100%', height: '500px' }}
         />
     )
 }
-
-export default VolcanoPlot

From c0a53a9a4bbaf17c54ae6e2237b818ddd6819482 Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Wed, 14 Jan 2026 15:25:36 -0300
Subject: [PATCH 36/47] Show thresholds

---
 ...ntialExpressionModalResultsVolcanoPlot.tsx |  8 ++++
 .../differential-expression/VolcanoPlot.tsx   | 42 +++++++++++++++++++
 2 files changed, 50 insertions(+)

diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
index 72461fa2..2df0c4c4 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
@@ -14,6 +14,7 @@ export const DifferentialExpressionModalResultsVolcanoPlot = (props: Differentia
     const [volcanoPoints, setVolcanoPoints] = useState<VolcanoPoint[]>([])
     const [fcThreshold, setFcThreshold] = useState<number>(1)
     const [pThreshold, setPThreshold] = useState<number>(0.05)
+    const [showThresholds, setShowThresholds] = useState(true)
 
     const getVolcanoPlotData = (signal: AbortSignal) => {
         if (!props.differentialExpressionAnalysisId) {
@@ -83,12 +84,19 @@ export const DifferentialExpressionModalResultsVolcanoPlot = (props: Differentia
                         onChange={(_, data) =>
                             setPThreshold(Number(data.value))}
                     />
+                    <Form.Checkbox
+                        label='Show thresholds'
+                        checked={showThresholds}
+                        onChange={(_, data) =>
+                            setShowThresholds(Boolean(data.checked))}
+                    />
                 </Form.Group>
             </Form>
 
             {/* 📊 Plot */}
             {volcanoPoints.length > 0 && (
                 <VolcanoPlot
+                    showThresholds={showThresholds}
                     data={volcanoPoints}
                     fcThreshold={fcThreshold}
                     pThreshold={pThreshold}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
index 022fb8ed..cfbb4452 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
@@ -12,12 +12,14 @@ interface VolcanoPlotProps {
     data: VolcanoPoint[]
     fcThreshold?: number
     pThreshold?: number
+    showThresholds: boolean
 }
 
 export const VolcanoPlot = ({
     data,
     fcThreshold = 1,
     pThreshold = 0.05,
+    showThresholds
 }: VolcanoPlotProps) => {
     const transformP = (p: number) => -Math.log10(p)
 
@@ -28,6 +30,45 @@ export const VolcanoPlot = ({
     const nonsignificant = data.filter(
         (d) => !(Math.abs(d.log2FC) >= fcThreshold && d.pValue <= pThreshold)
     )
+    const pLineY = transformP(pThreshold)
+
+    const thresholdShapes = showThresholds
+        ? [
+        // p-value threshold (horizontal)
+            {
+                type: 'line',
+                xref: 'paper',
+                x0: 0,
+                x1: 1,
+                yref: 'y',
+                y0: pLineY,
+                y1: pLineY,
+                line: { dash: 'dash', width: 1 },
+            },
+            // +log2FC threshold
+            {
+                type: 'line',
+                xref: 'x',
+                x0: fcThreshold,
+                x1: fcThreshold,
+                yref: 'paper',
+                y0: 0,
+                y1: 1,
+                line: { dash: 'dash', width: 1 },
+            },
+            // -log2FC threshold
+            {
+                type: 'line',
+                xref: 'x',
+                x0: -fcThreshold,
+                x1: -fcThreshold,
+                yref: 'paper',
+                y0: 0,
+                y1: 1,
+                line: { dash: 'dash', width: 1 },
+            },
+        ]
+        : []
 
     return (
         <Plot
@@ -79,6 +120,7 @@ export const VolcanoPlot = ({
                     title: { text: '-log10(p-value)', standoff: 10 },
                     zeroline: false,
                 },
+                shapes: thresholdShapes,
             }}
             config={{
                 responsive: true,

From 2ff6c0178b72b520d46a31d6ba71197b27fd0aef Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Wed, 14 Jan 2026 20:20:49 -0300
Subject: [PATCH 37/47] Refactor differential expression sources to use shared
 models

Removed DifferentialExpressionSource and DifferentialExpressionClinicalSource models in favor of using ExperimentSource and ExperimentClinicalSource from api_service. Updated related admin, views, tests, and model references. Added migrations to remove old models and update foreign keys. Improved download endpoint to support p-value filtering and filename suffix. Frontend SourcePopup now handles missing sources gracefully.
---
 ...ter_experiment_clinical_source_and_more.py | 142 +++++++++++++
 src/api_service/models.py                     |   8 +-
 ...study_clinical_patient_dataset_and_more.py |  80 +++++++
 src/differential_expression/admin.py          |  91 --------
 ...lexpressionsource_cgds_dataset_and_more.py |  47 ++++
 src/differential_expression/models.py         | 200 +-----------------
 .../tests/test_utils.py                       |  27 ++-
 src/differential_expression/views.py          |  39 +++-
 .../all-experiments-view/SourcePopup.tsx      |   5 +
 ...sticalproperties_gem_normality_and_more.py |  44 ++++
 10 files changed, 373 insertions(+), 310 deletions(-)
 create mode 100644 src/api_service/migrations/0062_alter_experiment_clinical_source_and_more.py
 create mode 100644 src/datasets_synchronization/migrations/0036_alter_cgdsstudy_clinical_patient_dataset_and_more.py
 create mode 100644 src/differential_expression/migrations/0005_remove_differentialexpressionsource_cgds_dataset_and_more.py
 create mode 100644 src/statistical_properties/migrations/0018_alter_sourcedatastatisticalproperties_gem_normality_and_more.py

diff --git a/src/api_service/migrations/0062_alter_experiment_clinical_source_and_more.py b/src/api_service/migrations/0062_alter_experiment_clinical_source_and_more.py
new file mode 100644
index 00000000..c86db344
--- /dev/null
+++ b/src/api_service/migrations/0062_alter_experiment_clinical_source_and_more.py
@@ -0,0 +1,142 @@
+# Generated by Django 4.2.19 on 2026-01-14 21:38
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "datasets_synchronization",
+            "0036_alter_cgdsstudy_clinical_patient_dataset_and_more",
+        ),
+        ("genes", "0002_auto_20210114_2331"),
+        ("user_files", "0015_alter_userfile_options"),
+        ("api_service", "0061_alter_experiment_shared_users"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="experiment",
+            name="clinical_source",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                related_name="experiments_as_clinical_source",
+                to="api_service.experimentclinicalsource",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="experiment",
+            name="gem_source",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="experiments_as_gem_source",
+                to="api_service.experimentsource",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="experiment",
+            name="mRNA_source",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="experiments_as_mrna_source",
+                to="api_service.experimentsource",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="experimentclinicalsource",
+            name="extra_cgds_dataset",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="experiment_clinical_sources_as_extra_cgds_dataset",
+                to="datasets_synchronization.cgdsdataset",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="experimentsource",
+            name="cgds_dataset",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="experiment_sources_as_cgds_dataset",
+                to="datasets_synchronization.cgdsdataset",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="experimentsource",
+            name="user_file",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="experiment_sources_as_user_file",
+                to="user_files.userfile",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="genecnacombination",
+            name="experiment",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="%(class)ss",
+                to="api_service.experiment",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="genecnacombination",
+            name="gene",
+            field=models.ForeignKey(
+                db_column="gene",
+                db_constraint=False,
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                related_name="%(class)ss_as_gene",
+                to="genes.gene",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="genemethylationcombination",
+            name="experiment",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="%(class)ss",
+                to="api_service.experiment",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="genemethylationcombination",
+            name="gene",
+            field=models.ForeignKey(
+                db_column="gene",
+                db_constraint=False,
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                related_name="%(class)ss_as_gene",
+                to="genes.gene",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="genemirnacombination",
+            name="experiment",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="%(class)ss",
+                to="api_service.experiment",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="genemirnacombination",
+            name="gene",
+            field=models.ForeignKey(
+                db_column="gene",
+                db_constraint=False,
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                related_name="%(class)ss_as_gene",
+                to="genes.gene",
+            ),
+        ),
+    ]
diff --git a/src/api_service/models.py b/src/api_service/models.py
index 8284560c..a6227a9b 100644
--- a/src/api_service/models.py
+++ b/src/api_service/models.py
@@ -335,7 +335,9 @@ def number_of_rows(self) -> int:
         """
         if self.user_file:
             return self.user_file.number_of_rows
-        return self.__get_cgds_datasets_joined_df().shape[0]
+        if self.cgds_dataset:
+            return self.__get_cgds_datasets_joined_df().shape[0]
+        return 0
 
     @property
     def number_of_samples(self) -> int:
@@ -345,7 +347,9 @@ def number_of_samples(self) -> int:
         """
         if self.user_file:
             return self.user_file.number_of_samples
-        return self.__get_cgds_datasets_joined_df().shape[1]
+        if self.cgds_dataset:
+            return self.__get_cgds_datasets_joined_df().shape[1]
+        return 0
 
 
 class Experiment(models.Model):
diff --git a/src/datasets_synchronization/migrations/0036_alter_cgdsstudy_clinical_patient_dataset_and_more.py b/src/datasets_synchronization/migrations/0036_alter_cgdsstudy_clinical_patient_dataset_and_more.py
new file mode 100644
index 00000000..189242c2
--- /dev/null
+++ b/src/datasets_synchronization/migrations/0036_alter_cgdsstudy_clinical_patient_dataset_and_more.py
@@ -0,0 +1,80 @@
+# Generated by Django 4.2.19 on 2026-01-14 21:38
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("datasets_synchronization", "0035_auto_20230922_2356"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="cgdsstudy",
+            name="clinical_patient_dataset",
+            field=models.OneToOneField(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                related_name="cgds_studies_as_clinical_patient_dataset",
+                to="datasets_synchronization.cgdsdataset",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cgdsstudy",
+            name="clinical_sample_dataset",
+            field=models.OneToOneField(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                related_name="cgds_studies_as_clinical_sample_dataset",
+                to="datasets_synchronization.cgdsdataset",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cgdsstudy",
+            name="cna_dataset",
+            field=models.OneToOneField(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                related_name="cgds_studies_as_cna_dataset",
+                to="datasets_synchronization.cgdsdataset",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cgdsstudy",
+            name="methylation_dataset",
+            field=models.OneToOneField(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                related_name="cgds_studies_as_methylation_dataset",
+                to="datasets_synchronization.cgdsdataset",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cgdsstudy",
+            name="mirna_dataset",
+            field=models.OneToOneField(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                related_name="cgds_studies_as_mirna_dataset",
+                to="datasets_synchronization.cgdsdataset",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cgdsstudy",
+            name="mrna_dataset",
+            field=models.OneToOneField(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                related_name="cgds_studies_as_mrna_dataset",
+                to="datasets_synchronization.cgdsdataset",
+            ),
+        ),
+    ]
diff --git a/src/differential_expression/admin.py b/src/differential_expression/admin.py
index 4a170b85..5199e7e2 100644
--- a/src/differential_expression/admin.py
+++ b/src/differential_expression/admin.py
@@ -1,101 +1,10 @@
 from django.contrib import admin
 from .models import (
-    DifferentialExpressionSource,
-    DifferentialExpressionClinicalSource,
     DifferentialExpressionExperiment,
     DifferentialExpressionExperimentResult
 )
 
 
-@admin.register(DifferentialExpressionSource)
-class DifferentialExpressionSourceAdmin(admin.ModelAdmin):
-    """Admin configuration for DifferentialExpressionSource model."""
-    
-    list_display = ('id', 'get_source_type', 'get_source_name', 'number_of_samples', 'number_of_rows')
-    list_filter = ('user_file__file_type',)  # Removed cgds_dataset__file_type as it might not exist
-    search_fields = ('user_file__name', 'cgds_dataset__name', 'user_file__user__username')
-    readonly_fields = ('id', 'number_of_samples', 'number_of_rows')
-    
-    fieldsets = (
-        ('Source Information', {
-            'fields': ('id', 'user_file', 'cgds_dataset')
-        }),
-        ('Statistics', {
-            'fields': ('number_of_samples', 'number_of_rows'),
-            'classes': ('collapse',)
-        }),
-    )
-    
-    def get_source_type(self, obj):
-        """Returns the type of source (UserFile or CGDS)."""
-        if obj.user_file:
-            return f"User File ({obj.user_file.file_type})"
-        elif obj.cgds_dataset:
-            return f"CGDS Dataset ({obj.cgds_dataset.file_type})"
-        return "No source"
-    get_source_type.short_description = 'Source Type'
-    
-    def get_source_name(self, obj):
-        """Returns the name of the source."""
-        try:
-            valid_source = obj.get_valid_source()
-            return valid_source.name if hasattr(valid_source, 'name') else str(valid_source)
-        except:
-            return "No source"
-    get_source_name.short_description = 'Source Name'
-
-
-@admin.register(DifferentialExpressionClinicalSource)
-class DifferentialExpressionClinicalSourceAdmin(admin.ModelAdmin):
-    """Admin configuration for DifferentialExpressionClinicalSource model."""
-    
-    list_display = ('id', 'get_source_type', 'get_source_name', 'get_attributes_count', 'number_of_samples')
-    list_filter = ('user_file__file_type',)  # Removed cgds_dataset__file_type as it might not exist
-    search_fields = ('user_file__name', 'cgds_dataset__name', 'user_file__user__username')
-    readonly_fields = ('id', 'number_of_samples', 'number_of_rows', 'get_attributes_count')
-    
-    fieldsets = (
-        ('Source Information', {
-            'fields': ('id', 'user_file', 'cgds_dataset', 'extra_cgds_dataset')
-        }),
-        ('Statistics', {
-            'fields': ('number_of_samples', 'number_of_rows', 'get_attributes_count'),
-            'classes': ('collapse',)
-        }),
-    )
-    
-    def get_source_type(self, obj):
-        """Returns the type of clinical source."""
-        if obj.user_file:
-            return f"User File ({obj.user_file.file_type})"
-        elif obj.cgds_dataset and obj.extra_cgds_dataset:
-            return "CGDS Clinical (Patient + Sample)"
-        elif obj.cgds_dataset:
-            return "CGDS Clinical (Patient only)"
-        return "No source"
-    get_source_type.short_description = 'Clinical Source Type'
-    
-    def get_source_name(self, obj):
-        """Returns the name of the clinical source."""
-        try:
-            if obj.user_file:
-                return obj.user_file.name
-            elif obj.cgds_dataset:
-                return obj.cgds_dataset.name
-            return "No source"
-        except:
-            return "No source"
-    get_source_name.short_description = 'Source Name'
-    
-    def get_attributes_count(self, obj):
-        """Returns the number of clinical attributes."""
-        try:
-            return len(obj.get_attributes())
-        except:
-            return 0
-    get_attributes_count.short_description = 'Clinical Attributes Count'
-
-
 @admin.register(DifferentialExpressionExperiment)
 class DifferentialExpressionExperimentAdmin(admin.ModelAdmin):
     """Admin configuration for DifferentialExpressionExperiment model."""
diff --git a/src/differential_expression/migrations/0005_remove_differentialexpressionsource_cgds_dataset_and_more.py b/src/differential_expression/migrations/0005_remove_differentialexpressionsource_cgds_dataset_and_more.py
new file mode 100644
index 00000000..508eaeb8
--- /dev/null
+++ b/src/differential_expression/migrations/0005_remove_differentialexpressionsource_cgds_dataset_and_more.py
@@ -0,0 +1,47 @@
+# Generated by Django 4.2.19 on 2026-01-14 22:02
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("api_service", "0062_alter_experiment_clinical_source_and_more"),
+        ("differential_expression", "0004_differentialexpressionexperiment_tool"),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="differentialexpressionsource",
+            name="cgds_dataset",
+        ),
+        migrations.RemoveField(
+            model_name="differentialexpressionsource",
+            name="user_file",
+        ),
+        migrations.AlterField(
+            model_name="differentialexpressionexperiment",
+            name="clinical_source",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="differential_expression_experiments_as_clinical",
+                to="api_service.experimentclinicalsource",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="differentialexpressionexperiment",
+            name="mrna_source",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="differential_expression_experiments_as_mrna",
+                to="api_service.experimentsource",
+            ),
+        ),
+        migrations.DeleteModel(
+            name="DifferentialExpressionClinicalSource",
+        ),
+        migrations.DeleteModel(
+            name="DifferentialExpressionSource",
+        ),
+    ]
diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index d63b5f38..e991efc2 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -2,201 +2,12 @@
 from django.contrib.auth import get_user_model
 from institutions.models import Institution
 from django.contrib.auth.models import User
-from typing import List, Optional, Iterable
 import pandas as pd
-import numpy as np
 import math
 from django.db.models import Q, QuerySet
 
 from api_service.websocket_functions import send_update_differential_expression_experiments_command
-from common.constants import PATIENT_ID_COLUMN
-
-
-class DifferentialExpressionSource(models.Model):
-    """
-    Represents a data source for differential expression experiments.
-    A source could be a user file or a CGDS Dataset.
-    """
-    user_file = models.ForeignKey(
-        'user_files.UserFile',
-        on_delete=models.CASCADE,
-        blank=True,
-        null=True,
-        related_name='differential_expression_sources'
-    )
-    cgds_dataset = models.ForeignKey(
-        'datasets_synchronization.CGDSDataset',
-        on_delete=models.CASCADE,
-        blank=True,
-        null=True,
-        related_name='differential_expression_sources'
-    )
-
-    def get_valid_source(self):
-        """
-        Gets the valid source depending on which has been uploaded by the user
-        @return: Valid source: a UserFile or a CGDSDataset
-        """
-        if self.user_file:
-            return self.user_file
-        elif self.cgds_dataset:
-            return self.cgds_dataset
-        else:
-            raise ValueError("No valid source found - both user_file and cgds_dataset are None")
-
-    def get_samples(self) -> List[str]:
-        """
-        Gets the samples of the source
-        @return: List with the samples
-        """
-        return self.get_valid_source().get_column_names()
-
-    def get_specific_row_and_columns(self, row: str, columns_idx: Optional[np.ndarray] = None) -> np.ndarray:
-        """
-        Gets a specific row and columns values from the source
-        @param row: Row's identifier to retrieve it
-        @param columns_idx: Indices of columns to filter, if None retrieves all the columns
-        @raise KeyError if the row data is empty
-        @return: List of values
-        """
-        row_data = self.get_valid_source().get_specific_row(row)
-        if row_data.size == 0:
-            raise KeyError(f"Row '{row}' not found in source")
-
-        if columns_idx is not None:
-            row_data = row_data[columns_idx]
-        return row_data
-
-    def get_df(self, only_matching: bool = False) -> pd.DataFrame:
-        """
-        Generates a DataFrame from the source
-        @param only_matching: If True only returns the molecules that are equal in both columns
-        @return: A DataFrame with the data to work
-        """
-        return self.get_valid_source().get_df(only_matching)
-
-    def get_df_in_chunks(self, only_matching: bool = False) -> Iterable[pd.DataFrame]:
-        """
-        Returns an Iterator of a DataFrame in divided in chunks from the source.
-        @param only_matching: If True only returns the molecules that are equal in both columns
-        @return: A DataFrame Iterator with the data to work.
-        """
-        return self.get_valid_source().get_df_in_chunks(only_matching)
-
-    @property
-    def number_of_rows(self) -> int:
-        """Number of rows in the source"""
-        return self.get_valid_source().number_of_rows
-
-    @property
-    def number_of_samples(self) -> int:
-        """Number of samples in the source"""
-        return self.get_valid_source().number_of_samples
-
-
-class DifferentialExpressionClinicalSource(DifferentialExpressionSource):
-    """
-    For clinical source of differential expression experiments. 
-    Needs an extra CGDSDataset field as cBioPortal has two clinical datasets:
-    patients data and samples data
-    """
-    extra_cgds_dataset = models.ForeignKey(
-        'datasets_synchronization.CGDSDataset',
-        on_delete=models.CASCADE,
-        blank=True,
-        null=True,
-        related_name='differential_expression_clinical_sources_extra'
-    )
-
-    def get_samples(self) -> List[str]:
-        """
-        Gets the samples of the clinical source
-        @return: List with the samples
-        """
-        if self.user_file:
-            # For user files, samples are in columns
-            return self.user_file.get_column_names()
-
-        # For CGDS datasets, returns a distinct concatenation of both source columns
-        # IMPORTANT: samples are in rows and attributes are in columns.
-        samples = self._get_cgds_datasets_joined_df().index
-        return list(set(samples))
-
-    def get_attributes(self) -> List[str]:
-        """
-        Gets the clinical attributes of the source without the special attributes like sample ids or patient ids
-        @return: List with the attributes
-        """
-        if self.user_file:
-            # For user files, attributes are in rows (transposed format)
-            return self.user_file.get_row_names()
-
-        # Returns a distinct concatenation of both source columns
-        columns_distinct = set()
-        if self.cgds_dataset:
-            first_clinical_source_columns = self.cgds_dataset.get_column_names()
-            columns_distinct.update(first_clinical_source_columns)
-
-        if self.extra_cgds_dataset:
-            second_clinical_source_columns = self.extra_cgds_dataset.get_column_names()
-            columns_distinct.update(second_clinical_source_columns)
-
-        # Remove special columns
-        special_columns = ['SAMPLE_ID', 'PATIENT_ID']
-        for column_to_remove in special_columns:
-            columns_distinct.discard(column_to_remove)
-        return list(columns_distinct)
-
-    def get_specific_samples_and_attributes(
-            self,
-            samples: Optional[List[str]],
-            clinical_attributes: List[str]
-    ) -> np.ndarray:
-        """
-        Gets specific samples and clinical attributes values from the source as a numpy array.
-        @param samples: List of samples to retrieve. If None, returns all the samples
-        @param clinical_attributes: List of clinical attributes to retrieve.
-        @return: Numpy array with values.
-        """
-        if self.user_file:
-            # For user files, use the user file's method
-            return self.user_file.get_specific_samples_and_attributes(samples, clinical_attributes)
-        else:
-            # For CGDS datasets, get the joined dataframe and filter
-            df = self._get_cgds_datasets_joined_df()
-            if samples is not None:
-                df = df.loc[samples]
-            result = df[clinical_attributes].to_numpy()
-            return result if len(clinical_attributes) > 1 else result[:, 0]
-
-    def _get_cgds_datasets_joined_df(self) -> pd.DataFrame | None:
-        """
-        Gets a joined DataFrame from both CGDS datasets (patient and sample data)
-        @return: Joined DataFrame
-        """
-        # This would need to be implemented based on how CGDS datasets are structured
-        # For now, return the main dataset
-        if self.cgds_dataset:
-            df1: pd.DataFrame = self.cgds_dataset.get_df(use_standard_column=False)
-            df2: pd.DataFrame = self.extra_cgds_dataset.get_df(use_standard_column=False)
-
-            # Sets the index to the patient ID column and joins both DataFrames
-            df1 = df1.reset_index().set_index([PATIENT_ID_COLUMN])
-            df2 = df2.reset_index().set_index([PATIENT_ID_COLUMN])
-
-            return df1.join(df2)
-
-        return None
-
-    def get_df(self, only_matching: bool = False) -> pd.DataFrame:
-        """
-        Generates a DataFrame from the clinical source
-        @return: A DataFrame with the clinical data
-        """
-        if self.user_file:
-            return self.user_file.get_df()
-        else:
-            return self._get_cgds_datasets_joined_df()
+from api_service.models import ExperimentSource, ExperimentClinicalSource
 
 
 class DifferentialExpressionExperimentState(models.IntegerChoices):
@@ -232,7 +43,7 @@ class DifferentialExpressionExperiment(models.Model):
     # Clinical and mRNA sources
     # These are used to link the experiment to the clinical and mRNA data sources
     clinical_source = models.ForeignKey(
-        'DifferentialExpressionClinicalSource',
+        'api_service.ExperimentClinicalSource',
         on_delete=models.CASCADE,
         null=False,
         blank=False,
@@ -240,7 +51,7 @@ class DifferentialExpressionExperiment(models.Model):
     )
 
     mrna_source = models.ForeignKey(
-        'DifferentialExpressionSource',
+        'api_service.ExperimentSource',
         on_delete=models.CASCADE,
         null=False,
         blank=False,
@@ -433,8 +244,9 @@ class Meta:
     def __str__(self):
         return f"{self.gene} - {self.experiment.name}"
 
-    @property
     def is_significant(self, p_threshold=0.05, fc_threshold=1.0):
         """Check if this gene is significantly differentially expressed."""
-        return (self.adj_p_val <= p_threshold and
+        return (self.adj_p_val is not None and
+                self.log_fc is not None and
+                self.adj_p_val <= p_threshold and
                 abs(self.log_fc) >= fc_threshold)
diff --git a/src/differential_expression/tests/test_utils.py b/src/differential_expression/tests/test_utils.py
index 56c9eb1b..3bdead8a 100644
--- a/src/differential_expression/tests/test_utils.py
+++ b/src/differential_expression/tests/test_utils.py
@@ -1,10 +1,9 @@
 import os
 from typing import Optional
 from django.contrib.auth.models import User
+from api_service.models import ExperimentSource, ExperimentClinicalSource
 from common.tests_utils import create_user_file
 from differential_expression.models import (
-    DifferentialExpressionSource,
-    DifferentialExpressionClinicalSource,
     DifferentialExpressionExperiment,
     DifferentialExpressionExperimentState,
     DifferentialExpressionTool
@@ -24,30 +23,30 @@ def get_test_file_path(filename: str) -> str:
     return file_path
 
 
-def create_differential_expression_source(user_file: UserFile) -> DifferentialExpressionSource:
+def create_differential_expression_source(user_file: UserFile) -> ExperimentSource:
     """
-    Creates a new instance of DifferentialExpressionSource saved in DB
-    @param user_file: UserFile to create the DifferentialExpressionSource
-    @return: DifferentialExpressionSource saved instance
+    Creates a new instance of ExperimentSource saved in DB
+    @param user_file: UserFile to create the ExperimentSource
+    @return: ExperimentSource saved instance
     """
-    source = DifferentialExpressionSource.objects.create(user_file=user_file)
+    source = ExperimentSource.objects.create(user_file=user_file)
     return source
 
 
-def create_differential_expression_clinical_source(user_file: UserFile) -> DifferentialExpressionClinicalSource:
+def create_differential_expression_clinical_source(user_file: UserFile) -> ExperimentClinicalSource:
     """
-    Creates a new instance of DifferentialExpressionClinicalSource saved in DB
-    @param user_file: UserFile to create the DifferentialExpressionClinicalSource
-    @return: DifferentialExpressionClinicalSource saved instance
+    Creates a new instance of ExperimentClinicalSource saved in DB
+    @param user_file: UserFile to create the ExperimentClinicalSource
+    @return: ExperimentClinicalSource saved instance
     """
-    source = DifferentialExpressionClinicalSource.objects.create(user_file=user_file)
+    source = ExperimentClinicalSource.objects.create(user_file=user_file)
     return source
 
 
 def create_test_differential_expression_experiment(
         name: str,
-        clinical_source: DifferentialExpressionClinicalSource,
-        mrna_source: DifferentialExpressionSource,
+        clinical_source: ExperimentClinicalSource,
+        mrna_source: ExperimentSource,
         user: User,
         state: DifferentialExpressionExperimentState = DifferentialExpressionExperimentState.WAITING_FOR_QUEUE,
         description: str = 'Test experiment',
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index c951b8b8..7a53f19b 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -23,14 +23,13 @@
 from common.functions import get_enum_from_value, get_intersection, encode_json_response_status
 from common.pagination import StandardResultsSetPagination
 from common.response import ResponseStatus
+from api_service.models import ExperimentClinicalSource, ExperimentSource
 from datasets_synchronization.models import CGDSDataset
 from datasets_synchronization.models import CGDSStudy
 from differential_expression.models import (
-    DifferentialExpressionClinicalSource,
     DifferentialExpressionExperiment,
-    DifferentialExpressionSource,
+    DifferentialExpressionExperimentState,
 )
-from differential_expression.models import DifferentialExpressionExperimentState
 from differential_expression.serializers import (
     DifferentialExpressionExperimentDetailSerializer,
     DifferentialExpressionExperimentResultSerializer,
@@ -49,13 +48,13 @@ def create_differential_expression_source(
         file_type: FileType,
         prefix: str
 ) -> tuple[
-    DifferentialExpressionSource | DifferentialExpressionClinicalSource | None, DifferentialExpressionClinicalSource | None
+    ExperimentSource | ExperimentClinicalSource | None, ExperimentClinicalSource | None
 ]:
     """
     Creates a Source object for differential expression experiments.
     """
     is_clinical = prefix == 'clinical'
-    source = DifferentialExpressionClinicalSource() if is_clinical else DifferentialExpressionSource()
+    source = ExperimentClinicalSource() if is_clinical else ExperimentSource()
     clinical_source = None
 
     if source_type == SourceType.NEW_DATASET.value:
@@ -278,7 +277,8 @@ class DifferentialExpressionResults(generics.ListAPIView):
     serializer_class = DifferentialExpressionExperimentResultSerializer
     permission_classes = [permissions.IsAuthenticated]
     pagination_class = StandardResultsSetPagination
-    filter_backends = [filters.OrderingFilter, DjangoFilterBackend]
+    filter_backends = [filters.SearchFilter, filters.OrderingFilter, DjangoFilterBackend]
+    search_fields = ['gene']
     ordering_fields = ['adj_p_val', 'log_fc', 'p_value', 'ave_expr']
     ordering = ['adj_p_val']  # Default ordering by adjusted p-value
 
@@ -726,6 +726,8 @@ def download_differential_expression_results(request, pk: int):
     """
     Downloads all the differential expression results for a specific experiment.
     Returns a TSV file with all results (no pagination).
+    Supports optional filtering via query parameter:
+    - p_value: adjusted p-value threshold (returns genes with adj_p_val <= p_value)
     """
     experiment = get_object_or_404(DifferentialExpressionExperiment, pk=pk)
 
@@ -737,8 +739,27 @@ def download_differential_expression_results(request, pk: int):
             experiment.shared_users.filter(id=user.id).exists()):
         return HttpResponse('Unauthorized', status=401)
 
-    # Get all results (no pagination)
-    results = experiment.results.all().order_by('adj_p_val')
+    # Get filter parameter from query string
+    p_value = request.GET.get('p_value')
+
+    # Apply filter if provided
+    if p_value is not None:
+        try:
+            p_value = float(p_value)
+        except ValueError:
+            return HttpResponse('Invalid p_value. Must be numeric.', status=400)
+
+        # Validate p_value
+        if p_value < 0 or p_value > 1:
+            return HttpResponse('p_value must be between 0 and 1', status=400)
+
+        # Filter results: adj_p_val <= p_value (significant genes)
+        results = experiment.results.filter(adj_p_val__lte=p_value).order_by('adj_p_val')
+        filename_suffix = f'_filtered_p{p_value}'
+    else:
+        # Get all results (no filtering)
+        results = experiment.results.all().order_by('adj_p_val')
+        filename_suffix = '_all'
 
     if not results.exists():
         return HttpResponse('No results found for this experiment', status=404)
@@ -763,6 +784,6 @@ def download_differential_expression_results(request, pk: int):
     # Generate HTTP response for file download
     response = HttpResponse(file_to_send, 'text/csv')
     response['Content-Length'] = file_to_send.size
-    response['Content-Disposition'] = f'attachment; filename="{experiment.name}_results.tsv"'
+    response['Content-Disposition'] = f'attachment; filename="{experiment.name}_results{filename_suffix}.tsv"'
 
     return response
diff --git a/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/SourcePopup.tsx b/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/SourcePopup.tsx
index caeafd61..0f110c51 100644
--- a/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/SourcePopup.tsx
+++ b/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/SourcePopup.tsx
@@ -30,6 +30,11 @@ export const SourcePopup = (props: SourcePopupProps) => {
     const isUserFile = props.source.user_file !== null
     const datasetObj = props.source.user_file ?? props.source.cgds_dataset
 
+    // If there's no valid source, don't render anything
+    if (!datasetObj) {
+        return null
+    }
+
     // Gets file's type description in plural to show the number of rows
     const datasetRowDescriptionInPlural = getFileRowDescriptionInPlural(datasetObj.file_type)
 
diff --git a/src/statistical_properties/migrations/0018_alter_sourcedatastatisticalproperties_gem_normality_and_more.py b/src/statistical_properties/migrations/0018_alter_sourcedatastatisticalproperties_gem_normality_and_more.py
new file mode 100644
index 00000000..c4e3bf98
--- /dev/null
+++ b/src/statistical_properties/migrations/0018_alter_sourcedatastatisticalproperties_gem_normality_and_more.py
@@ -0,0 +1,44 @@
+# Generated by Django 4.2.19 on 2026-01-14 21:38
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("api_service", "0062_alter_experiment_clinical_source_and_more"),
+        ("statistical_properties", "0017_alter_statisticalvalidation_state"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="sourcedatastatisticalproperties",
+            name="gem_normality",
+            field=models.OneToOneField(
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="source_data_statistical_properties_as_gem_normality",
+                to="statistical_properties.normalitytest",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="sourcedatastatisticalproperties",
+            name="gene_normality",
+            field=models.OneToOneField(
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="source_data_statistical_properties_as_gene_normality",
+                to="statistical_properties.normalitytest",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="statisticalvalidationsourceresult",
+            name="source",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="statistical_validation_source_results",
+                to="api_service.experimentsource",
+            ),
+        ),
+    ]

From 43812c7ad900dd768340a11aa193eb45a6a55f31 Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Thu, 15 Jan 2026 08:45:52 -0300
Subject: [PATCH 38/47] fixs pr updates

---
 ...ntialExpressionModalResultsVolcanoPlot.tsx | 21 ++++-------
 .../DifferentialExpressionPanel.tsx           |  4 ++
 .../differential-expression/types.ts          | 37 ++++++++++++++++++-
 .../frontend/src/utils/django_interfaces.ts   |  3 +-
 4 files changed, 49 insertions(+), 16 deletions(-)

diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
index 2df0c4c4..ff5523b0 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
@@ -16,16 +16,20 @@ export const DifferentialExpressionModalResultsVolcanoPlot = (props: Differentia
     const [pThreshold, setPThreshold] = useState<number>(0.05)
     const [showThresholds, setShowThresholds] = useState(true)
 
-    const getVolcanoPlotData = (signal: AbortSignal) => {
-        if (!props.differentialExpressionAnalysisId) {
+    useEffect(() => {
+        const id = props.differentialExpressionAnalysisId
+
+        if (!id) {
             return
         }
 
+        const controller = new AbortController()
+
         const url =
             `${urlDifferentialExpressionVolcanoData}/` +
             `${props.differentialExpressionAnalysisId}/`
 
-        ky.get(url, { retry: 5, signal }).then((response) => {
+        ky.get(url, { retry: 5, signal: controller.signal }).then((response) => {
             response.json().then((volcanoPointsResponse: VolcanoPoint[]) => {
                 setVolcanoPoints(volcanoPointsResponse)
             }).catch((err) => {
@@ -34,17 +38,6 @@ export const DifferentialExpressionModalResultsVolcanoPlot = (props: Differentia
         }).catch((err) => {
             console.error('Error getting volcanoPoints ->', err)
         })
-    }
-
-    useEffect(() => {
-        const id = props.differentialExpressionAnalysisId
-
-        if (!id) {
-            return
-        }
-
-        const controller = new AbortController()
-        getVolcanoPlotData(controller.signal)
 
         return () => {
             controller.abort()
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index 1a56dd91..31fa9ec3 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -31,6 +31,10 @@ interface DiferentialExpressionPanelState {
         isOpen: boolean
     }
 }
+/**
+ *  Differential Expression Panel component
+ * @returns JSX.Element
+ */
 
 export const DiferentialExpressionPanel = () => {
     const [state, setState] = useState<DiferentialExpressionPanelState>({
diff --git a/src/frontend/static/frontend/src/components/differential-expression/types.ts b/src/frontend/static/frontend/src/components/differential-expression/types.ts
index 0654df7c..0b7921cd 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/types.ts
+++ b/src/frontend/static/frontend/src/components/differential-expression/types.ts
@@ -4,48 +4,83 @@ import { DjangoExperimentSource, DjangoUser } from '../../utils/django_interface
  * Possible states for experiment evaluation
  */
 export enum DifferentialExpressionAnalysisExperimentState {
+    /* Finished successfully */
     COMPLETED = 1,
+    /* Finished with error */
     FINISHED_WITH_ERROR = 2,
+    /* Currently running */
     IN_PROCESS = 3,
+    /* Waiting in queue */
     WAITING_FOR_QUEUE = 4,
+    /* No samples in common between clinical and mRNA data */
     NO_SAMPLES_IN_COMMON = 5,
+    /* Manually stopping */
     STOPPING = 6,
+    /* Automatically stopped */
     STOPPED = 7,
+    /** Reached attempts limit */
     REACHED_ATTEMPTS_LIMIT = 8,
+    /* No features found */
     NO_FEATURES_FOUND = 9,
+    /* Empty dataset */
     EMPTY_DATASET = 10,
+    /* Operation timed out */
     TIMEOUT_EXCEEDED = 11,
 }
 
 export interface DifferentialExpressionAnalysis {
+    /* Unique identifier */
     id: number;
+    /* Name */
     name: string;
+    /* Description */
     description: string;
+    /* Analysis */
     tool: string;
+    /* Owner */
     user: DjangoUser;
+    /* Source of clinical data */
     clinical_source: DjangoExperimentSource;
+    /* Source of mRNA data */
     mrna_source: DjangoExperimentSource;
+    /* Current */
     state: DifferentialExpressionAnalysisExperimentState;
+    /* Human readable state */
     state_display: string;
+    /* Creation date */
     created_at: string;
+    /* Is public */
     is_public: boolean;
 }
 
 export interface DiffExpExperimentDetail {
+    /* Unique identifier */
     id: number;
+    /* Gene name */
     gene: string;
+    /* Average expression */
     ave_expr: number;
+    /* P-value */
     p_value: number;
+    /* Adjusted p-value */
     adj_p_val: number;
+    /* Log2 fold change */
     log_fc: number;
+    /* T statistic */
     t_statistic: number;
+    /* B statistic */
     b_statistic: number;
+    /* Is significant */
     is_significant: boolean;
 }
 
 export type VolcanoPoint = {
+    /* Unique identifier */
     id: string;
+    /* Optional label */
     label: string;
+    /* Log2 fold change */
     log2FC: number;
-    pValue: number; // adj.P.Val
+    /* P-value */
+    pValue: number;
 }
diff --git a/src/frontend/static/frontend/src/utils/django_interfaces.ts b/src/frontend/static/frontend/src/utils/django_interfaces.ts
index efcf887d..891a6d36 100644
--- a/src/frontend/static/frontend/src/utils/django_interfaces.ts
+++ b/src/frontend/static/frontend/src/utils/django_interfaces.ts
@@ -241,8 +241,9 @@ interface DjangoUserFile extends DjangoSimpleUserFile {
 }
 
 /**
- * Django Model api_service.ExperimentSource todo agregar opcional update_differential_expression_experiments
+ * Django Model api_service.ExperimentSource
  */
+// Todo: agregar opcional update_differential_expression_experiments
 interface DjangoExperimentSource {
     id?: number,
     user_file: DjangoSimpleUserFile,

From 84cb267d3d2a83ca7fb99f1552b3e77232b12a1f Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Tue, 20 Jan 2026 10:10:45 -0300
Subject: [PATCH 39/47] Add comment for useEffect in VolcanoPlot component

---
 .../DifferentialExpressionModalResultsVolcanoPlot.tsx            | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
index ff5523b0..7ef288ca 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
@@ -16,6 +16,7 @@ export const DifferentialExpressionModalResultsVolcanoPlot = (props: Differentia
     const [pThreshold, setPThreshold] = useState<number>(0.05)
     const [showThresholds, setShowThresholds] = useState(true)
 
+    /** Gets volano plot data on mount. */
     useEffect(() => {
         const id = props.differentialExpressionAnalysisId
 

From 0566d9dfda1b55c8f3d847949fdc1bbb7800bce3 Mon Sep 17 00:00:00 2001
From: Juan Nicolas Herrera <54152074+juanNH@users.noreply.github.com>
Date: Tue, 20 Jan 2026 11:39:45 -0300
Subject: [PATCH 40/47] fix pr comments

---
 .../DifferentialExpressionInputClinicalAttribute.tsx |  4 ++++
 .../DifferentialExpressionModalResults.tsx           | 12 +++++++++---
 ...DifferentialExpressionModalResultsVolcanoPlot.tsx |  5 +++--
 .../DifferentialExpressionPanel.tsx                  |  2 +-
 .../differential-expression/VolcanoPlot.tsx          |  5 +++++
 5 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
index 7349dfeb..4470cc9f 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
@@ -3,9 +3,13 @@ import { Form } from 'semantic-ui-react'
 import { InputLabel } from '../common/InputLabel'
 
 interface DifferentialExpressionInputClinicalAttributeProps {
+    /* List of clinical attributes available for selection */
     optionsClinicalAttributes: string[],
+    /* Currently selected clinical attribute */
     clinicalAttribute: string,
+    /* Callback when clinical attribute selection changes */
     onChange: (value: string) => void,
+    /* Whether the input is in editing mode */
     isEditing: boolean,
 }
 
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
index 89d11805..dbbebce8 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResults.tsx
@@ -1,17 +1,22 @@
-import React, { useMemo } from 'react'
+import React from 'react'
 import { DifferentialExpressionAnalysis } from './types'
 import { Icon, Modal, Tab, TabPane } from 'semantic-ui-react'
 import { DifferentialExpressionModalResultsTableView } from './DifferentialExpressionModalResultsTableView'
 import { DifferentialExpressionModalResultsVolcanoPlot } from './DifferentialExpressionModalResultsVolcanoPlot'
 
 interface DifferentialExpressionModalResultsProps {
+    /* Whether the results modal is open */
     isOpen: boolean
+    /* Differential expression analysis results to display */
     differentialExpressionAnalysis: DifferentialExpressionAnalysis | null
+    /* Callback to close the modal */
     closeModal: () => void
 }
 
+/* Differential expression results modal component */
 export const DifferentialExpressionModalResults = (props: DifferentialExpressionModalResultsProps) => {
-    const panes = useMemo(() => [
+    /* Tab panes for results modal */
+    const panes = [
         {
             menuItem: 'Table',
             render: () => (
@@ -28,7 +33,8 @@ export const DifferentialExpressionModalResults = (props: DifferentialExpression
                 </TabPane>
             )
         },
-    ], [props.differentialExpressionAnalysis?.id])
+    ]
+
     return (
         <Modal
             open={props.isOpen}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
index ff5523b0..913f41da 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
@@ -16,6 +16,7 @@ export const DifferentialExpressionModalResultsVolcanoPlot = (props: Differentia
     const [pThreshold, setPThreshold] = useState<number>(0.05)
     const [showThresholds, setShowThresholds] = useState(true)
 
+    /* Fetch volcano plot data if analysis ID is provided */
     useEffect(() => {
         const id = props.differentialExpressionAnalysisId
 
@@ -50,7 +51,7 @@ export const DifferentialExpressionModalResultsVolcanoPlot = (props: Differentia
         <div style={{ padding: 20 }}>
             <h3>Volcano Plot</h3>
 
-            {/* 🔽 Selects */}
+            {/* Selects */}
             <Form>
                 <Form.Group widths='equal'>
                     <Form.Select
@@ -86,7 +87,7 @@ export const DifferentialExpressionModalResultsVolcanoPlot = (props: Differentia
                 </Form.Group>
             </Form>
 
-            {/* 📊 Plot */}
+            {/* Plot */}
             {volcanoPoints.length > 0 && (
                 <VolcanoPlot
                     showThresholds={showThresholds}
diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
index 31fa9ec3..b0d5025e 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionPanel.tsx
@@ -31,11 +31,11 @@ interface DiferentialExpressionPanelState {
         isOpen: boolean
     }
 }
+
 /**
  *  Differential Expression Panel component
  * @returns JSX.Element
  */
-
 export const DiferentialExpressionPanel = () => {
     const [state, setState] = useState<DiferentialExpressionPanelState>({
         alert: getDefaultAlertProps(),
diff --git a/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
index cfbb4452..f1a666c9 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/VolcanoPlot.tsx
@@ -9,12 +9,17 @@ type VolcanoPoint = {
 }
 
 interface VolcanoPlotProps {
+    /* Data points for the volcano plot */
     data: VolcanoPoint[]
+    /* log2FC threshold for significance */
     fcThreshold?: number
+    /* p-value threshold for significance */
     pThreshold?: number
+    /* Whether to show threshold lines on the plot */
     showThresholds: boolean
 }
 
+/* Volcano plot component */
 export const VolcanoPlot = ({
     data,
     fcThreshold = 1,

From fd0832a186e747b5aeee62c512a8770c1e555f59 Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Tue, 20 Jan 2026 20:28:07 -0300
Subject: [PATCH 41/47] Refactor test data and endpoints for differential
 expression

Updated test CSV files to use realistic TCGA sample IDs and clinical attributes. Refactored test cases and utility functions to match new data format and attribute names. Changed API endpoint patterns for delete and update actions to '/delete/{pk}/' and '/update/{pk}/', and updated tests accordingly. Adjusted permission handling in tests to expect 403 Forbidden for unauthenticated requests. Added a new DifferentialExpressionRetrieve view for retrieving experiments with proper permission checks. Cleaned up and improved code style in models and serializers.
---
 src/differential_expression/models.py         |  34 ++--
 src/differential_expression/serializers.py    |  14 +-
 src/differential_expression/tasks.py          |   2 +-
 .../tests/test_models.py                      |  22 +--
 .../tests/test_utils.py                       |   2 +-
 .../tests/test_views.py                       | 152 +++---------------
 .../tests/tests_files/clinical_test.csv       |  11 +-
 .../tests/tests_files/mrna_test.csv           |  12 +-
 src/differential_expression/views.py          |  36 +++++
 9 files changed, 105 insertions(+), 180 deletions(-)

diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index e991efc2..4fa58e5a 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -128,9 +128,7 @@ def save(self, *args, **kwargs):
     def save_results(self, dataframe):
         """
         Save the differential expression DataFrame results.
-        
-        Args:
-            dataframe: pandas DataFrame with differential expression results
+        @param dataframe: pandas DataFrame with differential expression results.
         """
         # Clear existing results
         self.results.all().delete()
@@ -171,17 +169,15 @@ def get_results_dataframe(self):
         if not results.exists():
             return None
 
-        data = []
-        for result in results:
-            data.append({
-                'gene': result.gene,
-                'AveExpr': result.ave_expr,
-                'P.Value': result.p_value,
-                'adj.P.Val': result.adj_p_val,
-                'logFC': result.log_fc,
-                't': result.t_statistic,
-                'B': result.b_statistic
-            })
+        data = [{
+            'gene': result.gene,
+            'AveExpr': result.ave_expr,
+            'P.Value': result.p_value,
+            'adj.P.Val': result.adj_p_val,
+            'logFC': result.log_fc,
+            't': result.t_statistic,
+            'B': result.b_statistic
+        } for result in results]
 
         df = pd.DataFrame(data)
         df.set_index('gene', inplace=True)
@@ -190,13 +186,9 @@ def get_results_dataframe(self):
     def get_significant_genes(self, p_value_threshold=0.05, log_fc_threshold=1.0):
         """
         Get significantly differentially expressed genes.
-        
-        Args:
-            p_value_threshold: Maximum adjusted p-value (default 0.05)
-            log_fc_threshold: Minimum absolute log fold change (default 1.0)
-            
-        Returns:
-            QuerySet: QuerySet of DifferentialExpressionExperimentResult objects meeting the criteria
+        @param p_value_threshold: Maximum adjusted p-value (default 0.05).
+        @param log_fc_threshold: Minimum absolute log fold change (default 1.0).
+        @return QuerySet of DifferentialExpressionExperimentResult objects meeting the criteria.
         """
 
         return self.results.filter(
diff --git a/src/differential_expression/serializers.py b/src/differential_expression/serializers.py
index 533fe9e1..461aea0a 100644
--- a/src/differential_expression/serializers.py
+++ b/src/differential_expression/serializers.py
@@ -9,8 +9,8 @@
 from institutions.models import Institution
 
 
-class UserSimpleSerializer(serializers.ModelSerializer):
-    """Simple serializer for User model."""
+class UserSimpleForDiffExpExperiments(serializers.ModelSerializer):
+    """Simple serializer of User model for some differential expression analysis serializers."""
 
     class Meta:
         model = User
@@ -18,8 +18,8 @@ class Meta:
         read_only_fields = ['id', 'username', 'first_name', 'last_name', 'email']
 
 
-class InstitutionSimpleSerializer(serializers.ModelSerializer):
-    """Simple serializer for Institution model."""
+class InstitutionSimpleForDiffExpExperiments(serializers.ModelSerializer):
+    """Simple serializer of Institution model for some differential expression analysis serializers."""
 
     class Meta:
         model = Institution
@@ -68,7 +68,7 @@ class DifferentialExpressionExperimentListSerializer(serializers.ModelSerializer
     # Sources - using standard API serializers compatible with frontend interfaces
     clinical_source = ExperimentClinicalSourceSerializer(read_only=True)
     mrna_source = ExperimentSourceSerializer(read_only=True)
-    user = UserSimpleSerializer(read_only=True)
+    user = UserSimpleForDiffExpExperiments(read_only=True)
 
     # State information
     state_display = serializers.CharField(source='get_state_display', read_only=True)
@@ -97,7 +97,7 @@ class DifferentialExpressionExperimentSerializer(serializers.ModelSerializer):
     """
     Serializer for Differential Expression Experiment (General view with all fields).
     """
-    user = UserSimpleSerializer(read_only=True)
+    user = UserSimpleForDiffExpExperiments(read_only=True)
     clinical_source = ExperimentClinicalSourceSerializer(read_only=True)
     mrna_source = ExperimentSourceSerializer(read_only=True)
 
@@ -141,8 +141,6 @@ class DifferentialExpressionExperimentDetailSerializer(serializers.ModelSerializ
     Detailed serializer for Differential Expression Experiment (Detail view).
     Includes additional information like shared users and institutions.
     """
-    #shared_users = UserSimpleSerializer(many=True, read_only=True)
-    #shared_institutions = InstitutionSimpleSerializer(many=True, read_only=True)
 
     class Meta:#DifferentialExpressionExperimentSerializer.Meta):
         fields = '__all__'
diff --git a/src/differential_expression/tasks.py b/src/differential_expression/tasks.py
index 5359e837..4f17819e 100644
--- a/src/differential_expression/tasks.py
+++ b/src/differential_expression/tasks.py
@@ -48,7 +48,7 @@ def eval_differential_expression_experiment(self, experiment_pk: int, ):
 
         compute_differential_expression = DifferentialExpressionService(experiment, is_aborted=self.is_aborted)
         result = compute_differential_expression.perform_differential_expression()
-        print(f'Result of differential expression computation: {result}')
+
         total_execution_time = time.time() - start
         logging.info(f'DifferentialExpressionExperiment {experiment.pk} processed in {total_execution_time:.2f} seconds.')
         
diff --git a/src/differential_expression/tests/test_models.py b/src/differential_expression/tests/test_models.py
index effd04b2..8391c38d 100644
--- a/src/differential_expression/tests/test_models.py
+++ b/src/differential_expression/tests/test_models.py
@@ -120,7 +120,7 @@ def test_save_and_retrieve_results(self):
         # Assert results were saved correctly
         self.assertIsNotNone(retrieved_df)
         self.assertEqual(len(retrieved_df), 3)
-        self.assertEqual(list(retrieved_df.index), ['GENE_1', 'GENE_2', 'GENE_3'])
+        self.assertEqual(set(retrieved_df.index), {'GENE_1', 'GENE_2', 'GENE_3'})
 
         # Check specific values
         self.assertAlmostEqual(retrieved_df.loc['GENE_1', 'AveExpr'], 5.2, places=1)
@@ -264,10 +264,10 @@ def test_get_samples_from_mrna_source(self):
 
         samples = source.get_samples()
 
-        # Based on mrna_test.csv
+        # Based on mrna_test.csv (5 TCGA samples)
         self.assertEqual(len(samples), 5)
-        self.assertIn('SAMPLE_1', samples)
-        self.assertIn('SAMPLE_5', samples)
+        self.assertIn('TCGA-OR-A5J1-01', samples)
+        self.assertIn('TCGA-OR-A5J6-01', samples)
 
     def test_get_samples_from_clinical_source(self):
         """Test getting samples from clinical source"""
@@ -275,10 +275,10 @@ def test_get_samples_from_clinical_source(self):
 
         samples = source.get_samples()
 
-        # Based on clinical_test.csv
+        # Based on clinical_test.csv (5 TCGA samples)
         self.assertEqual(len(samples), 5)
-        self.assertIn('SAMPLE_1', samples)
-        self.assertIn('SAMPLE_5', samples)
+        self.assertIn('TCGA-OR-A5J1-01', samples)
+        self.assertIn('TCGA-OR-A5J6-01', samples)
 
     def test_get_clinical_attributes(self):
         """Test getting clinical attributes"""
@@ -286,9 +286,9 @@ def test_get_clinical_attributes(self):
 
         attributes = source.get_attributes()
 
-        # Based on clinical_test.csv (AGE, GENDER, STATUS, STAGE)
+        # Based on clinical_test.csv (SEX, AGE, TUMOR_STATUS, LATERALITY)
         self.assertEqual(len(attributes), 4)
+        self.assertIn('SEX', attributes)
         self.assertIn('AGE', attributes)
-        self.assertIn('GENDER', attributes)
-        self.assertIn('STATUS', attributes)
-        self.assertIn('STAGE', attributes)
+        self.assertIn('TUMOR_STATUS', attributes)
+        self.assertIn('LATERALITY', attributes)
diff --git a/src/differential_expression/tests/test_utils.py b/src/differential_expression/tests/test_utils.py
index 3bdead8a..d7633051 100644
--- a/src/differential_expression/tests/test_utils.py
+++ b/src/differential_expression/tests/test_utils.py
@@ -50,7 +50,7 @@ def create_test_differential_expression_experiment(
         user: User,
         state: DifferentialExpressionExperimentState = DifferentialExpressionExperimentState.WAITING_FOR_QUEUE,
         description: str = 'Test experiment',
-        clinical_attribute: str = 'STATUS',
+        clinical_attribute: str = 'TUMOR_STATUS',
         tool: DifferentialExpressionTool = DifferentialExpressionTool.DESEQ,
         threshold_percentile: float = 0.15,
         threshold: float = 0.0001,
diff --git a/src/differential_expression/tests/test_views.py b/src/differential_expression/tests/test_views.py
index 4b9fbece..4df7cc9c 100644
--- a/src/differential_expression/tests/test_views.py
+++ b/src/differential_expression/tests/test_views.py
@@ -70,7 +70,7 @@ def test_delete_experiment_success(self):
         self.client.force_authenticate(user=self.owner)
 
         # Delete the experiment
-        url = f'/differential-expression/{experiment.pk}/delete'
+        url = f'/differential-expression/delete/{experiment.pk}/'
         response = self.client.delete(url)
 
         # Assert response
@@ -97,7 +97,7 @@ def test_delete_experiment_not_owner(self):
         self.client.force_authenticate(user=self.other_user)
 
         # Try to delete the experiment
-        url = f'/differential-expression/{experiment.pk}/delete'
+        url = f'/differential-expression/delete/{experiment.pk}/'
         response = self.client.delete(url)
 
         # Assert forbidden
@@ -125,7 +125,7 @@ def test_delete_experiment_running_in_process(self):
         self.client.force_authenticate(user=self.owner)
 
         # Try to delete the experiment
-        url = f'/differential-expression/{experiment.pk}/delete'
+        url = f'/differential-expression/delete/{experiment.pk}/'
         response = self.client.delete(url)
 
         # Assert bad request
@@ -154,7 +154,7 @@ def test_delete_experiment_waiting_for_queue(self):
         self.client.force_authenticate(user=self.owner)
 
         # Try to delete the experiment
-        url = f'/differential-expression/{experiment.pk}/delete'
+        url = f'/differential-expression/delete/{experiment.pk}/'
         response = self.client.delete(url)
 
         # Assert bad request
@@ -182,7 +182,7 @@ def test_delete_experiment_stopping(self):
         self.client.force_authenticate(user=self.owner)
 
         # Try to delete the experiment
-        url = f'/differential-expression/{experiment.pk}/delete'
+        url = f'/differential-expression/delete/{experiment.pk}/'
         response = self.client.delete(url)
 
         # Assert bad request
@@ -209,7 +209,7 @@ def test_delete_experiment_stopped_success(self):
         self.client.force_authenticate(user=self.owner)
 
         # Delete the experiment
-        url = f'/differential-expression/{experiment.pk}/delete'
+        url = f'/differential-expression/delete/{experiment.pk}/'
         response = self.client.delete(url)
 
         # Assert success
@@ -236,7 +236,7 @@ def test_delete_experiment_with_error_success(self):
         self.client.force_authenticate(user=self.owner)
 
         # Delete the experiment
-        url = f'/differential-expression/{experiment.pk}/delete'
+        url = f'/differential-expression/delete/{experiment.pk}/'
         response = self.client.delete(url)
 
         # Assert success
@@ -262,11 +262,11 @@ def test_delete_experiment_not_authenticated(self):
         # Don't authenticate
 
         # Try to delete the experiment
-        url = f'/differential-expression/{experiment.pk}/delete'
+        url = f'/differential-expression/delete/{experiment.pk}/'
         response = self.client.delete(url)
 
         # Assert unauthorized
-        self.assertEqual(response.status_code, status.HTTP_401_UNAUTHORIZED)
+        self.assertEqual(response.status_code, status.HTTP_403_FORBIDDEN)
 
         # Assert experiment still exists
         self.assertTrue(
@@ -279,7 +279,7 @@ def test_delete_experiment_not_found(self):
         self.client.force_authenticate(user=self.owner)
 
         # Try to delete non-existent experiment
-        url = '/differential-expression/99999/delete'
+        url = '/differential-expression/delete/99999/'
         response = self.client.delete(url)
 
         # Assert not found
@@ -308,7 +308,7 @@ def test_delete_experiment_with_active_task(self, mock_async_result):
         self.client.force_authenticate(user=self.owner)
 
         # Delete the experiment
-        url = f'/differential-expression/{experiment.pk}/delete'
+        url = f'/differential-expression/delete/{experiment.pk}/'
         response = self.client.delete(url)
 
         # Assert success
@@ -391,110 +391,8 @@ def test_list_experiments_not_authenticated(self):
         # Don't authenticate
         response = self.client.get('/differential-expression/')
 
-        # Assert unauthorized
-        self.assertEqual(response.status_code, status.HTTP_401_UNAUTHORIZED)
-
-
-class DifferentialExpressionDetailTestCase(TestCase):
-    """Tests for DifferentialExpressionDetail endpoint"""
-
-    def setUp(self):
-        """Test setup"""
-        # Create test users
-        self.owner = User.objects.create_user(
-            username='owner',
-            email='owner@test.com',
-            password='testpass123'
-        )
-        self.other_user = User.objects.create_user(
-            username='other',
-            email='other@test.com',
-            password='testpass123'
-        )
-
-        # Create test files
-        self.mrna_file = create_user_file(
-            get_test_file_path('mrna_test.csv'),
-            'mRNA Test',
-            FileType.MRNA,
-            self.owner
-        )
-        self.clinical_file = create_user_file(
-            get_test_file_path('clinical_test.csv'),
-            'Clinical Test',
-            FileType.CLINICAL,
-            self.owner
-        )
-
-        # Create sources
-        self.mrna_source = create_differential_expression_source(self.mrna_file)
-        self.clinical_source = create_differential_expression_clinical_source(self.clinical_file)
-
-        # Create API client
-        self.client = APIClient()
-
-    def test_get_experiment_detail_as_owner(self):
-        """Test getting experiment detail as owner"""
-        experiment = create_test_differential_expression_experiment(
-            name='Test Experiment',
-            clinical_source=self.clinical_source,
-            mrna_source=self.mrna_source,
-            user=self.owner,
-            state=DifferentialExpressionExperimentState.COMPLETED
-        )
-
-        # Authenticate as owner
-        self.client.force_authenticate(user=self.owner)
-
-        # Get detail
-        response = self.client.get(f'/differential-expression/{experiment.pk}/')
-
-        # Assert success
-        self.assertEqual(response.status_code, status.HTTP_200_OK)
-        self.assertEqual(response.data['name'], 'Test Experiment')
-
-    def test_get_experiment_detail_not_owner_private(self):
-        """Test that non-owner cannot access private experiment"""
-        experiment = create_test_differential_expression_experiment(
-            name='Private Experiment',
-            clinical_source=self.clinical_source,
-            mrna_source=self.mrna_source,
-            user=self.owner,
-            state=DifferentialExpressionExperimentState.COMPLETED
-        )
-        experiment.is_public = False
-        experiment.save()
-
-        # Authenticate as other user
-        self.client.force_authenticate(user=self.other_user)
-
-        # Try to get detail
-        response = self.client.get(f'/differential-expression/{experiment.pk}/')
-
-        # Assert bad request (ValidationError returns 400)
-        self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
-
-    def test_get_experiment_detail_public(self):
-        """Test that anyone can access public experiment"""
-        experiment = create_test_differential_expression_experiment(
-            name='Public Experiment',
-            clinical_source=self.clinical_source,
-            mrna_source=self.mrna_source,
-            user=self.owner,
-            state=DifferentialExpressionExperimentState.COMPLETED
-        )
-        experiment.is_public = True
-        experiment.save()
-
-        # Authenticate as other user
-        self.client.force_authenticate(user=self.other_user)
-
-        # Get detail
-        response = self.client.get(f'/differential-expression/{experiment.pk}/')
-
-        # Assert success
-        self.assertEqual(response.status_code, status.HTTP_200_OK)
-        self.assertEqual(response.data['name'], 'Public Experiment')
+        # Assert forbidden (DRF returns 403 for unauthenticated requests)
+        self.assertEqual(response.status_code, status.HTTP_403_FORBIDDEN)
 
 
 class DifferentialExpressionUpdateTestCase(TestCase):
@@ -551,7 +449,7 @@ def test_update_experiment_name_and_description_success(self):
         self.client.force_authenticate(user=self.owner)
 
         # Update the experiment
-        url = f'/differential-expression/{experiment.pk}/update'
+        url = f'/differential-expression/update/{experiment.pk}/'
         data = {
             'name': 'Updated Name',
             'description': 'Updated Description'
@@ -569,7 +467,7 @@ def test_update_experiment_name_and_description_success(self):
         self.assertEqual(experiment.name, 'Updated Name')
         self.assertEqual(experiment.description, 'Updated Description')
 
-    def test_update_experiment_name_only_success(self):
+    def 3test_update_experiment_name_only_success(self):
         """Test successfully updating only the name"""
         # Create experiment
         experiment = create_test_differential_expression_experiment(
@@ -585,7 +483,7 @@ def test_update_experiment_name_only_success(self):
         self.client.force_authenticate(user=self.owner)
 
         # Update only the name
-        url = f'/differential-expression/{experiment.pk}/update'
+        url = f'/differential-expression/update/{experiment.pk}/'
         data = {'name': 'New Name Only'}
         response = self.client.patch(url, data, format='json')
 
@@ -616,7 +514,7 @@ def test_update_experiment_description_only_success(self):
         self.client.force_authenticate(user=self.owner)
 
         # Update only the description
-        url = f'/differential-expression/{experiment.pk}/update'
+        url = f'/differential-expression/update/{experiment.pk}/'
         data = {'description': 'New Description Only'}
         response = self.client.patch(url, data, format='json')
 
@@ -647,7 +545,7 @@ def test_update_experiment_not_owner(self):
         self.client.force_authenticate(user=self.other_user)
 
         # Try to update the experiment
-        url = f'/differential-expression/{experiment.pk}/update'
+        url = f'/differential-expression/update/{experiment.pk}/'
         data = {'name': 'Hacked Name'}
         response = self.client.patch(url, data, format='json')
 
@@ -675,7 +573,7 @@ def test_update_experiment_no_fields_provided(self):
         self.client.force_authenticate(user=self.owner)
 
         # Try to update with no fields
-        url = f'/differential-expression/{experiment.pk}/update'
+        url = f'/differential-expression/update/{experiment.pk}/'
         data = {}
         response = self.client.patch(url, data, format='json')
 
@@ -704,12 +602,12 @@ def test_update_experiment_not_authenticated(self):
         # Don't authenticate
 
         # Try to update the experiment
-        url = f'/differential-expression/{experiment.pk}/update'
+        url = f'/differential-expression/update/{experiment.pk}/'
         data = {'name': 'Hacked Name'}
         response = self.client.patch(url, data, format='json')
 
         # Assert unauthorized
-        self.assertEqual(response.status_code, status.HTTP_401_UNAUTHORIZED)
+        self.assertEqual(response.status_code, status.HTTP_403_FORBIDDEN)
 
         # Assert experiment was not updated
         experiment.refresh_from_db()
@@ -721,7 +619,7 @@ def test_update_experiment_not_found(self):
         self.client.force_authenticate(user=self.owner)
 
         # Try to update non-existent experiment
-        url = '/differential-expression/99999/update'
+        url = '/differential-expression/update/99999/'
         data = {'name': 'New Name'}
         response = self.client.patch(url, data, format='json')
 
@@ -744,7 +642,7 @@ def test_update_experiment_empty_name(self):
         self.client.force_authenticate(user=self.owner)
 
         # Try to update with empty name
-        url = f'/differential-expression/{experiment.pk}/update'
+        url = f'/differential-expression/update/{experiment.pk}/'
         data = {'name': ''}
         response = self.client.patch(url, data, format='json')
 
@@ -773,7 +671,7 @@ def test_update_experiment_empty_description(self):
         self.client.force_authenticate(user=self.owner)
 
         # Update with empty description (should be allowed)
-        url = f'/differential-expression/{experiment.pk}/update'
+        url = f'/differential-expression/update/{experiment.pk}/'
         data = {'description': ''}
         response = self.client.patch(url, data, format='json')
 
@@ -805,7 +703,7 @@ def test_update_running_experiment(self):
         self.client.force_authenticate(user=self.owner)
 
         # Update the experiment
-        url = f'/differential-expression/{experiment.pk}/update'
+        url = f'/differential-expression/update/{experiment.pk}/'
         data = {'name': 'Updated Name While Running'}
         response = self.client.patch(url, data, format='json')
 
diff --git a/src/differential_expression/tests/tests_files/clinical_test.csv b/src/differential_expression/tests/tests_files/clinical_test.csv
index 9103f936..86ff51dc 100644
--- a/src/differential_expression/tests/tests_files/clinical_test.csv
+++ b/src/differential_expression/tests/tests_files/clinical_test.csv
@@ -1,5 +1,6 @@
-,SAMPLE_1,SAMPLE_2,SAMPLE_3,SAMPLE_4,SAMPLE_5
-AGE,25,30,35,40,45
-GENDER,M,F,M,F,M
-STATUS,NORMAL,TUMOR,NORMAL,TUMOR,NORMAL
-STAGE,1,2,1,3,1
+SAMPLE_ID,SEX,AGE,TUMOR_STATUS,LATERALITY
+TCGA-OR-A5J1-01,Male,58,WITH TUMOR,Left
+TCGA-OR-A5J2-01,Female,44,WITH TUMOR,Left
+TCGA-OR-A5J3-01,Female,23,WITH TUMOR,Left
+TCGA-OR-A5J5-01,Male,30,WITH TUMOR,Right
+TCGA-OR-A5J6-01,Female,29,TUMOR FREE,Right
\ No newline at end of file
diff --git a/src/differential_expression/tests/tests_files/mrna_test.csv b/src/differential_expression/tests/tests_files/mrna_test.csv
index b3a6ffc5..0ef6a30b 100644
--- a/src/differential_expression/tests/tests_files/mrna_test.csv
+++ b/src/differential_expression/tests/tests_files/mrna_test.csv
@@ -1,6 +1,6 @@
-,SAMPLE_1,SAMPLE_2,SAMPLE_3,SAMPLE_4,SAMPLE_5
-GENE_1,5.2,6.1,5.8,7.2,6.5
-GENE_2,3.1,3.5,3.2,4.1,3.8
-GENE_3,8.5,9.2,8.8,10.1,9.5
-GENE_4,2.3,2.8,2.5,3.2,2.9
-GENE_5,6.7,7.3,6.9,8.1,7.5
+Standard_Symbol,TCGA-OR-A5J1-01,TCGA-OR-A5J2-01,TCGA-OR-A5J3-01,TCGA-OR-A5J5-01,TCGA-OR-A5J6-01
+LOC100130426,0.0,0.0,0.0,0.0,0.0
+HMGB1P1,149.1354,81.0777,86.4879,53.9117,66.9063
+TIMM23,2034.1018,1304.9251,1054.6586,2350.8908,1257.9864
+LOC155060,274.2555,199.302,348.3928,439.1944,149.2147
+SRP14P1,11.5274,5.2342,7.7026,6.1967,10.6183
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 7a53f19b..1d1d02cc 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -162,6 +162,42 @@ def get_queryset(self):
     pagination_class = StandardResultsSetPagination
     filter_backends = [filters.OrderingFilter, filters.SearchFilter, DjangoFilterBackend]
     search_fields = ['name', 'description']
+
+
+class DifferentialExpressionRetrieve(generics.RetrieveAPIView):
+    """
+    Endpoint to retrieve a single differential expression experiment by ID.
+    """
+    serializer_class = DifferentialExpressionExperimentListSerializer
+    permission_classes = [permissions.IsAuthenticated]
+
+    def get_queryset(self):
+        """
+        Returns experiments the user has access to.
+        """
+        user = self.request.user
+        return DifferentialExpressionExperiment.objects.filter(
+            Q(is_public=True) |
+            Q(user=user) |
+            Q(shared_institutions__institutionadministration__user=user) |
+            Q(shared_users=user)
+        ).distinct()
+
+    def get_object(self):
+        """
+        Retrieves the experiment and checks permissions.
+        """
+        experiment = get_object_or_404(DifferentialExpressionExperiment, pk=self.kwargs.get('pk'))
+        user = self.request.user
+
+        # Check if the user has access to the experiment
+        if not (experiment.is_public or
+                experiment.user == user or
+                experiment.shared_institutions.filter(institutionadministration__user=user).exists() or
+                experiment.shared_users.filter(id=user.id).exists()):
+            raise ValidationError('You do not have permission to access this experiment.')
+
+        return experiment
     filterset_fields = ['tool']
 
 

From 1232499e15040787146adac7a11140459511fdef Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Tue, 20 Jan 2026 21:07:52 -0300
Subject: [PATCH 42/47] Add integration tests and update test data files

Introduces integration tests for the differential expression analysis pipeline, including Celery task execution and result validation. Updates clinical and mRNA test CSV files to include 6 samples and expanded attributes, and adjusts related unit tests to match new test data structure. Fixes a typo in a test method name and sets the default clinical attribute to 'SEX' in test utilities.
---
 .../tests/test_integration.py                 | 224 ++++++++++++++++++
 .../tests/test_models.py                      |  24 +-
 .../tests/test_utils.py                       |   2 +-
 .../tests/test_views.py                       |   2 +-
 .../tests/tests_files/clinical_test.csv       |  13 +-
 .../tests/tests_files/mrna_test.csv           |  17 +-
 6 files changed, 256 insertions(+), 26 deletions(-)
 create mode 100644 src/differential_expression/tests/test_integration.py

diff --git a/src/differential_expression/tests/test_integration.py b/src/differential_expression/tests/test_integration.py
new file mode 100644
index 00000000..2f0ca64a
--- /dev/null
+++ b/src/differential_expression/tests/test_integration.py
@@ -0,0 +1,224 @@
+"""
+Integration tests for differential expression analysis.
+These tests execute the full pipeline including the Celery task and R/limma analysis.
+"""
+from unittest.mock import patch
+from django.test import TestCase, override_settings
+from django.contrib.auth.models import User
+from common.tests_utils import create_user_file
+from differential_expression.models import (
+    DifferentialExpressionExperiment,
+    DifferentialExpressionExperimentState,
+    DifferentialExpressionExperimentResult
+)
+from differential_expression.tests.test_utils import (
+    get_test_file_path,
+    create_differential_expression_source,
+    create_differential_expression_clinical_source,
+    create_test_differential_expression_experiment
+)
+from differential_expression.tasks import eval_differential_expression_experiment
+from user_files.models_choices import FileType
+
+
+def mock_is_aborted():
+    """Mock is_aborted to always return False for testing."""
+    return False
+
+
+@override_settings(
+    CELERY_TASK_ALWAYS_EAGER=True,
+    CELERY_TASK_EAGER_PROPAGATES=True
+)
+@patch.object(eval_differential_expression_experiment, 'is_aborted', mock_is_aborted)
+class DifferentialExpressionIntegrationTestCase(TestCase):
+    """
+    Integration tests that execute the full differential expression pipeline.
+    Uses CELERY_TASK_ALWAYS_EAGER to run Celery tasks synchronously.
+    """
+
+    def setUp(self):
+        """Test setup"""
+        # Create test user
+        self.user = User.objects.create_user(
+            username='testuser',
+            email='test@test.com',
+            password='testpass123'
+        )
+
+        # Create test files with real TCGA data
+        self.mrna_file = create_user_file(
+            get_test_file_path('mrna_test.csv'),
+            'mRNA Test',
+            FileType.MRNA,
+            self.user
+        )
+        self.clinical_file = create_user_file(
+            get_test_file_path('clinical_test.csv'),
+            'Clinical Test',
+            FileType.CLINICAL,
+            self.user
+        )
+
+        # Create sources
+        self.mrna_source = create_differential_expression_source(self.mrna_file)
+        self.clinical_source = create_differential_expression_clinical_source(self.clinical_file)
+
+    def test_full_differential_expression_analysis_by_sex(self):
+        """
+        Test the complete differential expression analysis pipeline.
+        Analyzes gene expression differences between Male and Female samples.
+        """
+        # Create experiment with SEX as the clinical attribute
+        experiment = create_test_differential_expression_experiment(
+            name='Integration Test - Sex Analysis',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user,
+            clinical_attribute='SEX',
+            state=DifferentialExpressionExperimentState.WAITING_FOR_QUEUE
+        )
+
+        # Verify initial state
+        self.assertEqual(experiment.state, DifferentialExpressionExperimentState.WAITING_FOR_QUEUE)
+        self.assertEqual(experiment.attempt, 0)
+
+        # Execute the Celery task synchronously
+        eval_differential_expression_experiment(experiment.pk)
+
+        # Refresh from database
+        experiment.refresh_from_db()
+
+        # Verify the experiment completed successfully
+        self.assertEqual(
+            experiment.state,
+            DifferentialExpressionExperimentState.COMPLETED,
+            f"Experiment should be COMPLETED but is {experiment.get_state_display()}"
+        )
+        self.assertEqual(experiment.attempt, 1)
+        self.assertGreater(experiment.execution_time, 0)
+
+        # Verify results were saved
+        results_count = experiment.results.count()
+        self.assertGreater(results_count, 0, "Should have differential expression results")
+
+        # Verify result structure
+        first_result = experiment.results.first()
+        self.assertIsNotNone(first_result.gene)
+        self.assertIsNotNone(first_result.p_value)
+        self.assertIsNotNone(first_result.adj_p_val)
+        self.assertIsNotNone(first_result.log_fc)
+
+    def test_differential_expression_results_dataframe(self):
+        """
+        Test that results can be retrieved as a pandas DataFrame.
+        """
+        # Create and run experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Integration Test - DataFrame Results',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user,
+            clinical_attribute='SEX',
+            state=DifferentialExpressionExperimentState.WAITING_FOR_QUEUE
+        )
+
+        # Execute the task
+        eval_differential_expression_experiment(experiment.pk)
+
+        # Refresh and get results as DataFrame
+        experiment.refresh_from_db()
+        results_df = experiment.get_results_dataframe()
+
+        # Verify DataFrame structure
+        self.assertIsNotNone(results_df)
+        self.assertGreater(len(results_df), 0)
+
+        # Check expected columns
+        expected_columns = ['AveExpr', 'P.Value', 'adj.P.Val', 'logFC', 't', 'B']
+        for col in expected_columns:
+            self.assertIn(col, results_df.columns, f"Missing column: {col}")
+
+        # Verify genes are in the index
+        self.assertTrue(len(results_df.index) > 0, "DataFrame should have genes as index")
+
+    def test_differential_expression_significant_genes(self):
+        """
+        Test filtering for significant differentially expressed genes.
+        """
+        # Create and run experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Integration Test - Significant Genes',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user,
+            clinical_attribute='SEX',
+            state=DifferentialExpressionExperimentState.WAITING_FOR_QUEUE
+        )
+
+        # Execute the task
+        eval_differential_expression_experiment(experiment.pk)
+
+        # Refresh from database
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.state, DifferentialExpressionExperimentState.COMPLETED)
+
+        # Test get_significant_genes with relaxed thresholds for test data
+        significant_genes = experiment.get_significant_genes(
+            p_value_threshold=1.0,  # Relaxed for small test dataset
+            log_fc_threshold=0.0
+        )
+
+        # Should return some results (we use relaxed thresholds)
+        self.assertIsNotNone(significant_genes)
+
+    def test_experiment_state_transitions(self):
+        """
+        Test that experiment goes through correct state transitions.
+        """
+        # Create experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Integration Test - State Transitions',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user,
+            clinical_attribute='SEX',
+            state=DifferentialExpressionExperimentState.WAITING_FOR_QUEUE
+        )
+
+        # Initial state
+        self.assertEqual(experiment.state, DifferentialExpressionExperimentState.WAITING_FOR_QUEUE)
+
+        # Execute task
+        eval_differential_expression_experiment(experiment.pk)
+
+        # Final state should be COMPLETED
+        experiment.refresh_from_db()
+        self.assertEqual(experiment.state, DifferentialExpressionExperimentState.COMPLETED)
+
+        # Attempt should be incremented
+        self.assertEqual(experiment.attempt, 1)
+
+    def test_experiment_execution_time_recorded(self):
+        """
+        Test that execution time is recorded after analysis.
+        """
+        # Create experiment
+        experiment = create_test_differential_expression_experiment(
+            name='Integration Test - Execution Time',
+            clinical_source=self.clinical_source,
+            mrna_source=self.mrna_source,
+            user=self.user,
+            clinical_attribute='SEX',
+            state=DifferentialExpressionExperimentState.WAITING_FOR_QUEUE
+        )
+
+        # Initial execution time should be 0
+        self.assertEqual(experiment.execution_time, 0.0)
+
+        # Execute task
+        eval_differential_expression_experiment(experiment.pk)
+
+        # Execution time should be recorded
+        experiment.refresh_from_db()
+        self.assertGreater(experiment.execution_time, 0)
\ No newline at end of file
diff --git a/src/differential_expression/tests/test_models.py b/src/differential_expression/tests/test_models.py
index 8391c38d..6a312dfe 100644
--- a/src/differential_expression/tests/test_models.py
+++ b/src/differential_expression/tests/test_models.py
@@ -264,10 +264,10 @@ def test_get_samples_from_mrna_source(self):
 
         samples = source.get_samples()
 
-        # Based on mrna_test.csv (5 TCGA samples)
-        self.assertEqual(len(samples), 5)
+        # Based on mrna_test.csv (6 TCGA samples as columns)
+        self.assertEqual(len(samples), 6)
         self.assertIn('TCGA-OR-A5J1-01', samples)
-        self.assertIn('TCGA-OR-A5J6-01', samples)
+        self.assertIn('TCGA-OR-A5J8-01', samples)
 
     def test_get_samples_from_clinical_source(self):
         """Test getting samples from clinical source"""
@@ -275,10 +275,10 @@ def test_get_samples_from_clinical_source(self):
 
         samples = source.get_samples()
 
-        # Based on clinical_test.csv (5 TCGA samples)
-        self.assertEqual(len(samples), 5)
-        self.assertIn('TCGA-OR-A5J1-01', samples)
-        self.assertIn('TCGA-OR-A5J6-01', samples)
+        # Based on clinical_test.csv (6 TCGA samples as row indices - PATIENT_ID)
+        self.assertEqual(len(samples), 6)
+        self.assertIn('TCGA-OR-A5J1', samples)
+        self.assertIn('TCGA-OR-A5J8', samples)
 
     def test_get_clinical_attributes(self):
         """Test getting clinical attributes"""
@@ -286,9 +286,9 @@ def test_get_clinical_attributes(self):
 
         attributes = source.get_attributes()
 
-        # Based on clinical_test.csv (SEX, AGE, TUMOR_STATUS, LATERALITY)
-        self.assertEqual(len(attributes), 4)
+        # Based on clinical_test.csv (OTHER_PATIENT_ID, SEX, OS_STATUS, OS_MONTHS, SAMPLE_ID, OTHER_SAMPLE_ID)
+        self.assertEqual(len(attributes), 6)
         self.assertIn('SEX', attributes)
-        self.assertIn('AGE', attributes)
-        self.assertIn('TUMOR_STATUS', attributes)
-        self.assertIn('LATERALITY', attributes)
+        self.assertIn('OS_STATUS', attributes)
+        self.assertIn('OS_MONTHS', attributes)
+        self.assertIn('SAMPLE_ID', attributes)
diff --git a/src/differential_expression/tests/test_utils.py b/src/differential_expression/tests/test_utils.py
index d7633051..dbd59d63 100644
--- a/src/differential_expression/tests/test_utils.py
+++ b/src/differential_expression/tests/test_utils.py
@@ -50,7 +50,7 @@ def create_test_differential_expression_experiment(
         user: User,
         state: DifferentialExpressionExperimentState = DifferentialExpressionExperimentState.WAITING_FOR_QUEUE,
         description: str = 'Test experiment',
-        clinical_attribute: str = 'TUMOR_STATUS',
+        clinical_attribute: str = 'SEX',
         tool: DifferentialExpressionTool = DifferentialExpressionTool.DESEQ,
         threshold_percentile: float = 0.15,
         threshold: float = 0.0001,
diff --git a/src/differential_expression/tests/test_views.py b/src/differential_expression/tests/test_views.py
index 4df7cc9c..1d7f17ae 100644
--- a/src/differential_expression/tests/test_views.py
+++ b/src/differential_expression/tests/test_views.py
@@ -467,7 +467,7 @@ def test_update_experiment_name_and_description_success(self):
         self.assertEqual(experiment.name, 'Updated Name')
         self.assertEqual(experiment.description, 'Updated Description')
 
-    def 3test_update_experiment_name_only_success(self):
+    def test_update_experiment_name_only_success(self):
         """Test successfully updating only the name"""
         # Create experiment
         experiment = create_test_differential_expression_experiment(
diff --git a/src/differential_expression/tests/tests_files/clinical_test.csv b/src/differential_expression/tests/tests_files/clinical_test.csv
index 86ff51dc..87d9867a 100644
--- a/src/differential_expression/tests/tests_files/clinical_test.csv
+++ b/src/differential_expression/tests/tests_files/clinical_test.csv
@@ -1,6 +1,7 @@
-SAMPLE_ID,SEX,AGE,TUMOR_STATUS,LATERALITY
-TCGA-OR-A5J1-01,Male,58,WITH TUMOR,Left
-TCGA-OR-A5J2-01,Female,44,WITH TUMOR,Left
-TCGA-OR-A5J3-01,Female,23,WITH TUMOR,Left
-TCGA-OR-A5J5-01,Male,30,WITH TUMOR,Right
-TCGA-OR-A5J6-01,Female,29,TUMOR FREE,Right
\ No newline at end of file
+PATIENT_ID,OTHER_PATIENT_ID,SEX,OS_STATUS,OS_MONTHS,SAMPLE_ID,OTHER_SAMPLE_ID
+TCGA-OR-A5J1,B3164F7B-C826-4E08-9EE6-8FF96D29B913,Male,1:DECEASED,44.51,TCGA-OR-A5J1-01,E4038EBB-6E6D-44B1-84AD-E35AAFCA7B70
+TCGA-OR-A5J2,8E7C2E31-D085-4B75-A970-162526DD07A0,Female,1:DECEASED,55.09,TCGA-OR-A5J2-01,46B7EB7C-E5F7-476D-A68C-5972F947445F
+TCGA-OR-A5J3,DFD687BC-6E69-42F7-AF94-D17FC150D1A1,Female,0:LIVING,68.69,TCGA-OR-A5J3-01,1FB59B6F-53C0-4B14-82CC-77CD55C67AD6
+TCGA-OR-A5J5,802DBD0D-EF07-4C91-AB8D-1DD39532E947,Male,1:DECEASED,11.99,TCGA-OR-A5J5-01,C6214F9B-35C8-424C-B6FE-BEC1A9317C0A
+TCGA-OR-A5J6,C8898B42-B704-45A0-9829-144B98F416E0,Female,0:LIVING,88.8,TCGA-OR-A5J6-01,C0C9DD1B-98B1-4A20-8927-3C0B75A4559E
+TCGA-OR-A5J8,08E0D412-D4D8-4D13-B792-A4DD0BD9EC2B,Male,1:DECEASED,19.02,TCGA-OR-A5J8-01,2F47F06E-8F76-440E-BBCE-B7C90635A59E
diff --git a/src/differential_expression/tests/tests_files/mrna_test.csv b/src/differential_expression/tests/tests_files/mrna_test.csv
index 0ef6a30b..ac8c756e 100644
--- a/src/differential_expression/tests/tests_files/mrna_test.csv
+++ b/src/differential_expression/tests/tests_files/mrna_test.csv
@@ -1,6 +1,11 @@
-Standard_Symbol,TCGA-OR-A5J1-01,TCGA-OR-A5J2-01,TCGA-OR-A5J3-01,TCGA-OR-A5J5-01,TCGA-OR-A5J6-01
-LOC100130426,0.0,0.0,0.0,0.0,0.0
-HMGB1P1,149.1354,81.0777,86.4879,53.9117,66.9063
-TIMM23,2034.1018,1304.9251,1054.6586,2350.8908,1257.9864
-LOC155060,274.2555,199.302,348.3928,439.1944,149.2147
-SRP14P1,11.5274,5.2342,7.7026,6.1967,10.6183
+Standard_Symbol,TCGA-OR-A5J1-01,TCGA-OR-A5J2-01,TCGA-OR-A5J3-01,TCGA-OR-A5J5-01,TCGA-OR-A5J6-01,TCGA-OR-A5J8-01
+LOC100130426,0.0,0.0,0.0,0.0,0.0,0.0
+UBE2Q2P3,3.2661,2.6815,1.7301,0.0,0.0,1.4422
+HMGB1P1,149.1354,81.0777,86.4879,53.9117,66.9063,94.9316
+TIMM23,2034.1018,1304.9251,1054.6586,2350.8908,1257.9864,995.0269
+MOXD2,0.0,0.0,0.0,0.0,0.0,0.0
+LOC155060,274.2555,199.302,348.3928,439.1944,149.2147,377.9528
+RNU12-2P,1.4409,0.0,0.5925,0.7746,0.0,1.6577
+EZHIP,17.7714,0.4026,0.5925,0.7746,0.0,1.2433
+EFCAB8,0.0,0.4026,0.5925,0.7746,2.7943,0.8288
+SRP14P1,11.5274,5.2342,7.7026,6.1967,10.6183,5.3875

From 4725074b37b6157adc210e39a337ac4b883e9b30 Mon Sep 17 00:00:00 2001
From: Hernan <HernanGuillermo.Zabala@Alumnos.UAI.edu.ar>
Date: Tue, 20 Jan 2026 23:11:52 -0300
Subject: [PATCH 43/47] Remove utils.py and update views.py error handling

Deleted the unused utils.py file. In views.py, removed redundant experiment_id type validation and updated comments to English for clarity.
---
 src/differential_expression/utils.py |  0
 src/differential_expression/views.py | 15 +++++----------
 2 files changed, 5 insertions(+), 10 deletions(-)
 delete mode 100644 src/differential_expression/utils.py

diff --git a/src/differential_expression/utils.py b/src/differential_expression/utils.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/src/differential_expression/views.py b/src/differential_expression/views.py
index 1d1d02cc..d0629550 100644
--- a/src/differential_expression/views.py
+++ b/src/differential_expression/views.py
@@ -140,7 +140,7 @@ def get_queryset(self) -> DifferentialExpressionExperiment:
 class DifferentialExpressionList(generics.ListAPIView):
     """
     Endpoint to list all differential expression experiments.
-    Devuelve solo los campos: id, Name, Description, Date, State, Sources y si es publico.
+    Returns only the fields: id, Name, Description, Date, State, Sources and if it is public.
     """
 
     def get_queryset(self):
@@ -393,11 +393,6 @@ def get(request: Request):
         if not experiment_id:
             raise ValidationError('experimentId is required.')
 
-        try:
-            experiment_id = int(experiment_id)
-        except (ValueError, TypeError) as exc:
-            raise ValidationError('Invalid experimentId') from exc
-
         experiment = get_object_or_404(DifferentialExpressionExperiment, pk=experiment_id)
 
         user = request.user
@@ -411,7 +406,7 @@ def get(request: Request):
         if not experiment.task_id:
             return Response({'ok': False, 'detail': 'The experiment does not have an associated task.'})
 
-        # Si ya no está en curso, no hay nada que detener
+        # If it's no running, there's nothing to stop
         if experiment.state in [
             DifferentialExpressionExperimentState.COMPLETED,
             DifferentialExpressionExperimentState.STOPPED,
@@ -424,14 +419,14 @@ def get(request: Request):
         ]:
             return Response({'ok': False, 'detail': f'The experiment is not running. Status: {experiment.state}'})
 
-        # Intentar abortar la tarea AbortableTask
+        # Try to abort the AbortableTask
         try:
             async_res = AbortableAsyncResult(experiment.task_id)
-            aborted = async_res.abort()  # Señala a la tarea que debe abortar (self.is_aborted() == True)
+            aborted = async_res.abort()  # Signals the task to abort (self.is_aborted() == True)
         except Exception as e:
             return Response({'ok': False, 'detail': f'The task could not be stopped: {e}'})
 
-        # Marcar el experimento como STOPPING; la tarea lo marcará como STOPPED en el finally
+        # Mark the experiment as STOPPING; the task will mark it as STOPPED in the finally block
         experiment.state = DifferentialExpressionExperimentState.STOPPING
         experiment.save(update_fields=['state'])
 

From 229fccf4429b6a7b5199fa68bbd1c19a92e0461f Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Thu, 22 Jan 2026 17:54:39 -0300
Subject: [PATCH 44/47] Refactor admin configuration for models

---
 src/differential_expression/admin.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/src/differential_expression/admin.py b/src/differential_expression/admin.py
index 5199e7e2..99df8606 100644
--- a/src/differential_expression/admin.py
+++ b/src/differential_expression/admin.py
@@ -89,9 +89,3 @@ def is_significant_display(self, obj):
             return False
     is_significant_display.short_description = 'Is Significant (p<0.05, |logFC|>1)'
     is_significant_display.boolean = True
-
-
-
-admin.site.site_header = "Multiomix Administration"
-admin.site.site_title = "Multiomix Admin"
-admin.site.index_title = "Welcome to Multiomix Administration"

From c35fa6cdd7a89bfa0d43a73814a4d244902d1d65 Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Thu, 22 Jan 2026 17:55:24 -0300
Subject: [PATCH 45/47] Refactor DifferentialExpressionExperiment model

Refactor DifferentialExpressionExperiment and related classes to improve code structure and maintainability.
---
 src/differential_expression/models.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/differential_expression/models.py b/src/differential_expression/models.py
index 4fa58e5a..d07f4d44 100644
--- a/src/differential_expression/models.py
+++ b/src/differential_expression/models.py
@@ -110,16 +110,11 @@ def __str__(self):
 
     def save(self, *args, **kwargs):
         """
-        Override the save method to ensure that the name is unique.
         Every time the experiment status changes, uses websockets to update state in the frontend.
         """
         if not self.name:
             raise ValueError("Experiment name cannot be empty.")
 
-        # # Ensure the name is unique
-        # if DifferentialExpressionExperiment.objects.filter(name=self.name).exists():
-        #     raise ValueError(f"An experiment with the name '{self.name}' already exists.")
-
         super().save(*args, **kwargs)
 
         # Sends a websockets message to update the experiment state in the frontend
@@ -242,3 +237,4 @@ def is_significant(self, p_threshold=0.05, fc_threshold=1.0):
                 self.log_fc is not None and
                 self.adj_p_val <= p_threshold and
                 abs(self.log_fc) >= fc_threshold)
+

From 372fa0bfbf6c3f8aee14b6b463d848e6caa1a877 Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Thu, 22 Jan 2026 17:58:40 -0300
Subject: [PATCH 46/47] Add JSDoc comment for
 DifferentialExpressionInputClinicalAttribute

Added JSDoc comment to the DifferentialExpressionInputClinicalAttribute component.
---
 .../DifferentialExpressionInputClinicalAttribute.tsx         | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
index 4470cc9f..b1ff4dc7 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionInputClinicalAttribute.tsx
@@ -13,6 +13,11 @@ interface DifferentialExpressionInputClinicalAttributeProps {
     isEditing: boolean,
 }
 
+/**
+ * Renders a Select to select a clinical attribute.
+ * @param props Component props.
+ * @returns Component.
+ */
 export const DifferentialExpressionInputClinicalAttribute = (props: DifferentialExpressionInputClinicalAttributeProps) => {
     return (
         <>

From 022cac78a78ba212fcf078202b3da7b10ae56231 Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Thu, 22 Jan 2026 17:59:39 -0300
Subject: [PATCH 47/47] Define props and add documentation for Volcano plot

Added prop types and documentation for the Volcano plot component.
---
 .../DifferentialExpressionModalResultsVolcanoPlot.tsx       | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
index 913f41da..656c2112 100644
--- a/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
+++ b/src/frontend/static/frontend/src/components/differential-expression/DifferentialExpressionModalResultsVolcanoPlot.tsx
@@ -6,10 +6,16 @@ import { Form } from 'semantic-ui-react'
 
 declare const urlDifferentialExpressionVolcanoData: string
 
+/** DifferentialExpressionModalResultsVolcanoPlot props. */
 interface DifferentialExpressionModalResultsVolcanoPlotProps {
     differentialExpressionAnalysisId?: number;
 }
 
+/**
+ * Renders a Volcano plot.
+ * @param props Component props.
+ * @returns Component.
+ */
 export const DifferentialExpressionModalResultsVolcanoPlot = (props: DifferentialExpressionModalResultsVolcanoPlotProps) => {
     const [volcanoPoints, setVolcanoPoints] = useState<VolcanoPoint[]>([])
     const [fcThreshold, setFcThreshold] = useState<number>(1)