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

chipseq: A package for analyzing chipseq data

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews ChIPSeq, Coverage, DataImport, QualityControl, Sequencing, Software
Version 1.55.0
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
See More
Suggests BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr
Linking To
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_1.55.0.tar.gz
Windows Binary
macOS Binary (x86_64) chipseq_1.55.0.tgz
macOS Binary (arm64) chipseq_1.55.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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