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