BaalChIP
This is the development version of BaalChIP; for the stable release version, see BaalChIP.
All Bioconductor versions of BaalChIP
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4
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.
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 gmail.com>
Citation
From within R, enter citation("BaalChIP"):
Ines de Santiago, Wei Liu, Ke Yuan, Martin O'Reilly, Chandra SR Chilamakuri, Bruce Ponder, Kerstin Meyer, Florian Markowetz. BaalChIP: BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes. doi:10.18129/B9.bioc.BaalChIP, R package version 1.39.0, https://bioconductor.org/packages/BaalChIP.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("BaalChIP")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.39.0 |
| License | Artistic-2.0 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.4 (R-3.3) (9 years) |
| Downloads rank | 1297 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, ChIPSeq, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/BaalChIP/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BaalChIP")| BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | BaalChIP_1.39.0.tar.gz |
| Windows binary (x86_64) | BaalChIP_1.39.0.zip |
| macOS binary (arm64) | BaalChIP_1.39.0.tgz |
| macOS binary (x86_64) | BaalChIP_1.39.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BaalChIP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BaalChIP |
| Package Downloads Report | Download Stats |
Dependencies
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