To install this package, start R and enter:

## try http if https is not available

In most cases, you don't need to download the package archive at all.



Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges.

Bioconductor version: Release (3.1)

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages

Author: Lihua Julie Zhu, Jianhong Ou, Herve Pages, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green

Maintainer: Lihua Julie Zhu <julie.zhu at>, Jianhong Ou <Jianhong.ou at>

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


To install this package, start R and enter:

## try http if https is not available


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



PDF R Script ChIPpeakAnno Vignette
PDF   Reference Manual
Text   NEWS


biocViews Annotation, ChIPSeq, ChIPchip, Software
Version 3.2.2
In Bioconductor since BioC 2.5 (R-2.10) (6 years)
License GPL (>= 2)
Depends R (>= 2.10), grid, VennDiagram, biomaRt, IRanges, Biostrings, GenomicRanges
Imports BiocGenerics(>= 0.1.0), GO.db, BSgenome, GenomicFeatures, AnnotationDbi, limma, multtest, RBGL, graph, BiocInstaller, stats
Suggests reactome.db, BSgenome.Ecoli.NCBI.20080805,,, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, RUnit, BiocStyle, rtracklayer
Depends On Me ggtut, REDseq
Imports Me FunciSNP, REDseq
Suggests Me ggtut, oneChannelGUI, R3CPET, RIPSeeker
Build Report  

Package Archives

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

Package Source ChIPpeakAnno_3.2.2.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard) ChIPpeakAnno_3.2.2.tgz
Mac OS X 10.9 (Mavericks) ChIPpeakAnno_3.2.2.tgz
Subversion source (username/password: readonly)
Git source
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center