This is the released version of BaalChIP; for the devel version, see BaalChIP.
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomesBioconductor version: Release (3.21)
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, entercitation("BaalChIP")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BaalChIP")Follow Installation instructions to use this package in your R session.
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