BaalChIP
This package is for version 3.17 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: 3.17
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("BaalChIP")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | Bayesian, ChIPSeq, Sequencing, Software |
| Version | 1.26.0 |
| 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 |
See More
| Suggests | RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BaalChIP_1.26.0.tar.gz |
| Windows Binary | BaalChIP_1.26.0.zip |
| macOS Binary (x86_64) | BaalChIP_1.26.0.tgz |
| macOS Binary (arm64) | BaalChIP_1.26.0.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 3.17 | Source Archive |