chipseq

DOI: 10.18129/B9.bioc.chipseq  

chipseq: A package for analyzing chipseq data

Bioconductor version: Release (3.17)

Tools for helping process short read data for chipseq experiments.

Author: Deepayan Sarkar [aut], Robert Gentleman [aut], Michael Lawrence [aut], Zizhen Yao [aut], Oluwabukola Bamigbade [ctb] (Converted vignette from Sweave to R Markdown / HTML.), Bioconductor Package Maintainer [cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("chipseq")

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("chipseq")

 

HTML	R Script	Some Basic Analysis of ChIP-Seq Data
PDF		Reference Manual

Details

biocViews	ChIPSeq, Coverage, DataImport, QualityControl, Sequencing, Software
Version	1.50.0
In Bioconductor since	BioC 2.5 (R-2.10) (14 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), methods, BiocGenerics(>= 0.1.0), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), GenomicRanges(>= 1.31.8), ShortRead
Imports	methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead
LinkingTo
Suggests	BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	ChIPQC, CopywriteR, HTSeqGenie, soGGi, transcriptR
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	chipseq_1.50.0.tar.gz
Windows Binary	chipseq_1.50.0.zip
macOS Binary (x86_64)	chipseq_1.50.0.tgz
macOS Binary (arm64)	chipseq_1.50.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/chipseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/chipseq
Bioc Package Browser	https://code.bioconductor.org/browse/chipseq/
Package Short Url	https://bioconductor.org/packages/chipseq/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive