TCGA repository contains the code and processes for the analysis presented in Single-cell chromatin accessibility, revealing malignant regulatory programs in primary human cancers. Data associated with the publication is being uploaded to https://gdc.cancer.gov/about-data/publications/TCGA-ATAC-Seq-2024 (publication page). Each folder here contains the analysis code for each main figure and the associated supplemental figures. Each folder contains the description for the code and the analysis.