GUIdedRNA

A comprehensive Shiny application for guided RNA-seq analysis including quality control, preprocessing, dimensionality reduction, clustering, and cell type annotation.

Features and workflow

1. Setup: Upload 10X Genomics data (or any .mtx/barcode/feature combination) or folder containing multiple datasets
2. Sample Information: Add metadata and sample attributes
3. Quality Control: Set filtering parameters and visualize QC metrics
4. Preprocessing: Run doublet removal, unannotated gene removal, and ambient RNA correction
5. LSI Round 1: Initial dimensionality reduction
6. Broad Clustering: Assign broad cell types using marker genes and visualize any gene expression in UMAP
7. LSI Round 2: Refined analysis on cell type subsets
8. Final Clustering: Detailed cell type annotation and visualize any gene expression in UMAP per subcluster
9. Integration: Combine all results into final annotations
10. Download: Export processed data and results

Installation and regular use

For Regular Users (Recommended) No technical knowledge required - just double-click and wait!

Windows/IOS/Linux Users

1. Download this repository (green "Code" button → "Download ZIP")
2. Extract to your Desktop
3. Download and install https://www.docker.com/products/docker-desktop/
4. Run Docker Desktop
5. Run the appropriate script in extracted GUIdedRNA map:
   • Windows: Double-click INSTALL_AND_RUN.bat
   • IOS/Linux: Double-click INSTALL_AND_RUN.sh
6. Let Docker build container (5-15 minutes)
7. If browser does not open simply go to http://localhost:3838

After docker container is build once, subsequently running app is instantaneous and can be done through docker desktop or by double-clicking INSTALL_AND_RUN again. Refresh browser if connection cannot be found.

Tip

When using app, your directories to upload data and set the output directory are likely found by changing volume: home to root >> files are found under host_drives.

Note

On IOS/Linux if you can't double click INSTALL_AND_RUN.sh you might need to run the following in command line to make the file executable.

**Open Terminal/Command Line**
cd Desktop/GUIdedRNA
chmod +x INSTALL_AND_RUN_IOSLIN.sh  
./INSTALL_AND_RUN_IOSLIN.sh  

For Advanced Users & Developers

WSL2 Users (Windows Subsystem for Linux)
If you need Windows drive access and advanced volume mounting:

Run through command line with ADVANCED_DEPLOY.sh
If working through command line simply open in any browser at http://localhost:3838

Installation of GUIdedRNA library and use through IDE

Install prerequisites

# Install devtools
install.packages("devtools", 'fields', 'KernSmooth', 'ROCR', 'parallel')

# Install BiocManager dependencies
install.packages("BiocManager", repos = "https://cloud.r-project.org")
BiocManager::install(c("sparseMatrixStats", "AnnotationDbi", "edgeR", "GenomicRanges", "GenomicFeatures", "org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg38.knownGene", "celda", "decontX"))

# Install GUIdedRNA
devtools::install_github("chris-mcginnis-ucsf/DoubletFinder")
devtools::install_github("VUbels/GUIdedRNA")

Usage

R Package

library(GUIdedRNA)

# Launch the application
launch_GUIdedRNA()

# Launch with custom settings
launch_GUIdedRNA(port = 8080, host = "localhost")

Docker

# Using docker-compose (recommended)
docker-compose up

# Or manual Docker
docker build -t guidedrna .
docker run -p 3838:3838 -v ./data:/data -v ./output:/output guidedrna

Requirements

• R >= 4.0.0
• Seurat >= 5.0.0
• Docker (for containerized deployment)

Support

For issues and questions, please visit our GitHub Issues page.