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

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Bioconductor version: Development (3.20)

The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.

Author: Lihua Julie Zhu, Jianhong Ou, Jun Yu, Kai Hu, Haibo Liu, Junhui Li, Hervé Pagès, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe, Michael Green

Maintainer: Jianhong Ou <jianhong.ou at>, Lihua Julie Zhu <julie.zhu at>, Kai Hu < at>, Junhui Li < at>

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


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:

ChIPpeakAnno: annotate, visualize, and compare peak data HTML R Script
Reference Manual PDF


biocViews Annotation, ChIPSeq, ChIPchip, Software
Version 3.39.0
In Bioconductor since BioC 2.5 (R-2.10) (14.5 years)
License GPL (>= 2)
Depends R (>= 3.5), methods, IRanges(>= 2.13.12), GenomicRanges(>= 1.31.8), S4Vectors(>= 0.17.25)
Imports AnnotationDbi, BiocGenerics(>= 0.1.0), Biostrings(>= 2.47.6), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils, universalmotif, stringr, tibble, tidyr, data.table, scales, ensembldb
System Requirements
See More
Suggests AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19,,, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache
Linking To
Depends On Me REDseq, csawBook
Imports Me ATACseqQC, DEScan2, GUIDEseq
Suggests Me hicVennDiagram, R3CPET, seqsetvis, chipseqDB
Links To Me
Build Report Build Report

Package Archives

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

Source Package ChIPpeakAnno_3.39.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) ChIPpeakAnno_3.39.0.tgz
macOS Binary (arm64) ChIPpeakAnno_3.39.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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