Comprehensive characterization of the inflammatory ecosystems in immunotherapy-induced adverse events versus chronic inflammatory diseases

This repository contains code used in the study "Comprehensive characterization of the inflammatory ecosystems in immunotherapy-induced adverse events versus chronic inflammatory diseases."

Here are the details for each notebook.

1) CIA_step1.sc_process_qc_metadata

• single-cell RNA-seq dataset quality control and pre-processing
• Cell type annotation
• Sample metadata curation

2) CIA_step2.NMF

• Analysis pipeline for non-negative matrix factorization

3) CIA_step3.data_integration

• Data integration and harmonization using SCANVI

4) CIA_step4.apply_cellstates_to_other_datasets

• Applying cell states to independent single-cell and bulk transcriptome datasets

5) CIA_step5.Spatial_analysis

• Spatial transcriptomics pipeline