BaalChIP

This package is for version 3.9 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: 3.9

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 "3.6") 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	1.10.0
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
System Requirements
URL

Suggests	RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

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

Source Package	BaalChIP_1.10.0.tar.gz
Windows Binary	BaalChIP_1.10.0.zip
Mac OS X 10.11 (El Capitan)	BaalChIP_1.10.0.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
Old Source Packages for BioC 3.9	Source Archive