This repository contains supplementary materials for the research 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 CNA-TC and immune-TC for each spot in spatial transcriptomic datasets from 10xGenomics