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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
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This package is for version 3.4 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: 3.4
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, Bruce Ponder, Kerstin Meyer, Florian Markowetz
Maintainer: Ines de Santiago <ines.deSantiago at cruk.cam.ac.uk>
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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bayesian, ChIPSeq, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (0.5 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 |
| 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.
| Package Source | BaalChIP_1.0.0.tar.gz |
| Windows Binary | BaalChIP_1.0.0.zip |
| Mac OS X 10.9 (Mavericks) | BaalChIP_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/BaalChIP/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/BaalChIP/ |
| Package Downloads Report | Download Stats |
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