Association of copy number alterations with the immune transcriptomic landscape in cancer

This repository contains supplementary materials and data for the paper "Association of copy number alterations with the immune transcriptomic landscape in cancer". The materials are organized in the following folders:

• 00_code: code to reproduce the analysis
• 01_ica_datasets: transcriptional components, sample mixing matrix activities, and gene set enrichment analysis results of the GPL570, ARCHS4, and TCGA datasets
• 02_ica_cna_tc: identified CNA-TCs and their captured CNA regions, genomic plots of CNA-TCs
• 03_ica_immune_tc: identified immune-TCs, list of immune gene sets
• 04_ica_tc_dataset_overlap: reproducibility results of CNA-TCs and immune-TCs across datasets
• 05_immune_gene_occurences: frequency of genes with high gene weight in immune-TCs, list potential novel immune involved ORFs
• 06_projection_immune_tc_datasets: GPL570 and TCGA cancer samples corrected mixing matrix activitiy for CNA-TCs and immune-TCs of the other dataset
• 07_inferred_cna_profiles: TACNA profiles and CNA burden per cancer sample
• 08_cna_burden_immune_tc_association: cancer sample associations of CNA burden, individual CNAs, and single gene CNAs with immune-TCs
• 09_projection_single_cell: cell type activity of immune-TCs in a single-cell tumor immune atlas for precision oncology  
• 10_projection_spatial_transcriptomics: activity of immune-TCs and CNA-TCs for each spot in spatial transcriptomic datasets from 10x Genomics
• 11_immunotherapy_response: gene expression data, sample annotation, and mixing matrix of projected GPL570 immune- TCs and CNA-TCs for 13 immunotherapy response datasets with predictive performance