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@Moldia

Molecular Diagnostics (Mats Nilsson research group)

Scripts and softwares used in research

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  1. Xenium_benchmarking Xenium_benchmarking Public

    Code used to benchmark Xenium

    Jupyter Notebook 76 13

  2. multi_padlock_design multi_padlock_design Public

    Padlock design pipeline for multiplexed assay with multiple probes per target in cDNA-based expression profiling

    Python 15 15

  3. InSituCNV InSituCNV Public

    Jupyter Notebook 12

  4. Lee_2023 Lee_2023 Public

    All the code described in the Lee et al. (2023) paper

    Jupyter Notebook 10 10

  5. in_situ_seq in_situ_seq Public

    Basic analysis pipeline for in situ sequencing

    MATLAB 5 1

  6. Tools Tools Public

    Repository containing all the preprocessing and analysis tools generated in Molecular Diagnosis group, Science for Life Laboratories, Stockholm University, Sweden

    MATLAB 4 3

Repositories

Showing 10 of 36 repositories
  • ISS2025 Public Forked from mgcizzu/ISS2025

    Major update of the ISS analysis code

    Moldia/ISS2025’s past year of commit activity
    Jupyter Notebook 1 MIT 10 4 0 Updated Feb 5, 2026
  • CRC_Shedding_Xenium Public

    Colorectal Cancer analysis of 2 shedders and 2 non-shedders samples using Xenium Human Colon Gene Expression Panel.

    Moldia/CRC_Shedding_Xenium’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Dec 5, 2025
  • PLP_directRNA_design_V2 Public
    Moldia/PLP_directRNA_design_V2’s past year of commit activity
    Jupyter Notebook 0 0 8 1 Updated Oct 16, 2025
  • InSituCNV Public
    Moldia/InSituCNV’s past year of commit activity
    Jupyter Notebook 12 0 1 0 Updated Oct 2, 2025
  • adult_lung_DiscovAIR_spatial Public

    Code used to analyze the spatial datasets included in Firsova et al. 2024

    Moldia/adult_lung_DiscovAIR_spatial’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Sep 22, 2025
  • scrinshot_converter Public Forked from mgcizzu/scrinshot_converter

    Code to convert SCRINSHOT probes designed with Oligo Design Toolkit to Nilsson barcodes.

    Moldia/scrinshot_converter’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Sep 4, 2025
  • Lee_2023 Public

    All the code described in the Lee et al. (2023) paper

    Moldia/Lee_2023’s past year of commit activity
    Jupyter Notebook 10 10 3 0 Updated May 30, 2025
  • multi_padlock_design Public

    Padlock design pipeline for multiplexed assay with multiple probes per target in cDNA-based expression profiling

    Moldia/multi_padlock_design’s past year of commit activity
    Python 15 MIT 15 8 0 Updated Jul 11, 2024
  • Xenium_benchmarking Public

    Code used to benchmark Xenium

    Moldia/Xenium_benchmarking’s past year of commit activity
    Jupyter Notebook 76 13 10 0 Updated Jun 30, 2024
  • GBmap_ISS Public

    Code used in the publication "Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma" for the analysis of ISS data

    Moldia/GBmap_ISS’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Apr 22, 2024
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