chipseq

This is the development version of chipseq; for the stable release version, see chipseq.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

chipseq: A package for analyzing chipseq data

Bioconductor version: Development (3.24)

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")):

Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao. chipseq: chipseq: A package for analyzing chipseq data. doi:10.18129/B9.bioc.chipseq, R package version 1.63.0, https://bioconductor.org/packages/chipseq.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, Coverage, DataImport, QualityControl, Sequencing, Software
Version	1.63.0
In Bioconductor since	BioC 2.5 (R-2.10) (17 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

Suggests	BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr
Linking To
Enhances
Depends On Me
Imports Me	ChIPQC, transcriptR
Suggests Me	profileplyr
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	chipseq_1.63.0.tar.gz
Windows Binary (x86_64)	chipseq_1.63.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	chipseq_1.63.0.tgz
macOS Binary (sonoma-arm64)	chipseq_1.63.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/chipseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/chipseq
Package Short Url	https://bioconductor.org/packages/chipseq/
Package Downloads Report	Download Stats