DOI: 10.18129/B9.bioc.BaalChIP  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BaalChIP.

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

Bioconductor version: 3.16

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.

Author: Ines de Santiago, Wei Liu, Ke Yuan, Martin O'Reilly, Chandra SR Chilamakuri, Bruce Ponder, Kerstin Meyer, Florian Markowetz

Maintainer: Ines de Santiago <inesdesantiago at>

Citation (from within R, enter citation("BaalChIP")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Analyzing ChIP-seq and FAIRE-seq data with the BaalChIP package
PDF   Reference Manual
Text   NEWS


biocViews Bayesian, ChIPSeq, Sequencing, Software
Version 1.24.0
In Bioconductor since BioC 3.4 (R-3.3) (6.5 years)
License Artistic-2.0
Depends R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools
Imports GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats
Suggests RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BaalChIP_1.24.0.tar.gz
Windows Binary
macOS Binary (x86_64) BaalChIP_1.24.0.tgz
macOS Binary (arm64) BaalChIP_1.24.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: