BaalChIP
This is the released version of BaalChIP; for the devel version, see BaalChIP.
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Bayesian, ChIPSeq, Sequencing, Software |
| Version | 1.38.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 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_1.38.0.tar.gz |
| Windows Binary (x86_64) | BaalChIP_1.38.0.zip |
| macOS Binary (big-sur-x86_64) | BaalChIP_1.38.0.tgz |
| macOS Binary (sonoma-arm64) | BaalChIP_1.38.0.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 3.23 | Source Archive |