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

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.

Package details

AuthorInes de Santiago, Wei Liu, Ke Yuan, Martin O'Reilly, Chandra SR Chilamakuri, Bruce Ponder, Kerstin Meyer, Florian Markowetz
Bioconductor views Bayesian ChIPSeq Sequencing Software
MaintainerInes de Santiago <>
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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BaalChIP documentation built on Nov. 8, 2020, 5:23 p.m.