DOI: 10.18129/B9.bioc.chipseq  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see chipseq.

chipseq: A package for analyzing chipseq data

Bioconductor version: 3.16

Tools for helping process short read data for chipseq experiments

Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao

Maintainer: Bioconductor Package Maintainer <maintainer at>

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


To install this package, start R (version "4.2") and enter:

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


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:



PDF R Script A Sample ChIP-Seq analysis workflow
PDF   Reference Manual


biocViews ChIPSeq, Coverage, DataImport, QualityControl, Sequencing, Software
Version 1.48.0
In Bioconductor since BioC 2.5 (R-2.10) (13.5 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
Suggests BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene
Depends On Me
Imports Me ChIPQC, CopywriteR, HTSeqGenie, soGGi, transcriptR
Suggests Me
Links To Me
Build Report  

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

Source Package chipseq_1.48.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) chipseq_1.48.0.tgz
macOS Binary (arm64) chipseq_1.48.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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