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

Bioconductor version: Release (3.19)

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 "4.4") 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:

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


biocViews Bayesian, ChIPSeq, Sequencing, Software
Version 1.30.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
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Suggests RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package BaalChIP_1.30.0.tar.gz
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macOS Binary (x86_64) BaalChIP_1.30.0.tgz
macOS Binary (arm64) BaalChIP_1.30.0.tgz
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