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chipseq

chipseq: A package for analyzing chipseq data


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("chipseq")):

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

Details

biocViews ChIPSeq, Coverage, DataImport, QualityControl, Sequencing, Software
Version 1.52.0
In Bioconductor since BioC 2.5 (R-2.10) (14.5 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
System Requirements
URL
See More
Suggests BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr
Linking To
Enhances
Depends On Me
Imports Me ChIPQC, HTSeqGenie, soGGi, transcriptR
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package chipseq_1.52.0.tar.gz
Windows Binary chipseq_1.52.0.zip
macOS Binary (x86_64) chipseq_1.52.0.tgz
macOS Binary (arm64) chipseq_1.52.0.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