BaalChIP

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Bioconductor version: 3.24 · Package version: 1.39.0

The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BaalChIP")