CAR-T Associated Enterocolitis Analysis Scripts

Repository containing code used to analyze single-cell RNA-seq data published in
Data available under GEO accession number GSE322796

Software & Packages

Single-Cell Analysis Pathway Enrichment & Cell-Cell Communication

Cell Frequency Visualisation

Repository Structure

CART-Enterocolitis-Analysis-Scripts/
├── R Scripts/
│   ├── 01_QC.Rmd                               # Ambient RNA removal, doublet detection, QC filtering
│   ├── 02_Integration.Rmd                      # Batch correction
│   ├── 03_Clustering.Rmd                       # Global clustering, annotation, condition UMAPs
│   ├── 04_Subclustering_Stroma.Rmd             # Sub-clustering workflow (stromal shown; same workflow applied to T cells, myeloid, B cells, plasma cells, epithelial, and endothelial subsets)
│   ├── 05_DEGs_and_GSEA_Stroma_Condition.Rmd   # Condition-wise DEGs + GSEA
│   ├── 06_CLR_CellFreq_Stroma.Rmd              # CLR cell-frequency analysis + forest plots (stromal shown; same workflow applied globally  and to all other subsets)
│   ├── 07_Figs_Stroma.Rmd                      # Figures for stromal subset (bubble plots, stacked bars, condition plots, etc.)
│   └── 08_CAR_Mapping_and_Figs.Rmd             # Certomics CAR+ cell mapping onto T cell subset, heatmaps, pie plots, etc.
│   └── 09_CellChat.Rmd                         # Sample-wise CellChat that was aggregated and analyzed further using regression model
├── sessionInfo.md                              # Full R session information and package versions
└── README.md