Dataset and code for article "Expanded detection and impact of BAP1 alterations in cancer"

Dataset and code for article titled "Expanded detection and impact of BAP1 alterations in cancer". Includes Singularity image and Nextflow code for somatic variant calling pipeline. Also includes figure code (qmd, html, and pdf formats), analysis code (qmd), and public raw and processed data of reasonable file size. Controlled-access data and large file size data (e.g., combined dataset of pan-cancer individual RNA-seq files) must be downloaded separately from the TCGA Genomic Data Commons or PanCanAtlas Publication pages. R code written in R version 4.4.1 and provided with R environment (renv) information.