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BaalChIP

This is the development version of BaalChIP; for the stable release version, see BaalChIP.

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

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Bayesian, ChIPSeq, Sequencing, Software
Version 1.27.0
In Bioconductor since BioC 3.4 (R-3.3) (7 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
Linking To
Suggests RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
System Requirements
Enhances
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Imports Me
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Package Archives

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

Source Package BaalChIP_1.27.0.tar.gz
Windows Binary BaalChIP_1.27.0.zip (64-bit only)
macOS Binary (x86_64) BaalChIP_1.27.0.tgz
macOS Binary (arm64) BaalChIP_1.27.0.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