To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BaalChIP")

In most cases, you don't need to download the package archive at all.

BaalChIP

DOI: 10.18129/B9.bioc.BaalChIP    

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

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BaalChIP")

Documentation

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

Details

biocViews Bayesian, ChIPSeq, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
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
LinkingTo
Suggests RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package BaalChIP_1.4.0.tar.gz
Windows Binary BaalChIP_1.4.0.zip
Mac OS X 10.11 (El Capitan) BaalChIP_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BaalChIP
Package Short Url http://bioconductor.org/packages/BaalChIP/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: