BaalChIP

This package is for version 3.19 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: 3.19

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 gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("BaalChIP")

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

Documentation

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

browseVignettes("BaalChIP")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, ChIPSeq, Sequencing, Software
Version	1.30.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 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
System Requirements
URL

Suggests	RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
Linking To
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Build Report	Build Report

Package Archives

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

Source Package	BaalChIP_1.30.0.tar.gz
Windows Binary (x86_64)	BaalChIP_1.30.0.zip
macOS Binary (x86_64)	BaalChIP_1.30.0.tgz
macOS Binary (arm64)	BaalChIP_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BaalChIP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BaalChIP
Bioc Package Browser	https://code.bioconductor.org/browse/BaalChIP/
Package Short Url	https://bioconductor.org/packages/BaalChIP/
Package Downloads Report	Download Stats