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Association analysis of genomic regions based on permutation tests

Bioconductor version: Release (3.19)

regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

Author: Anna Diez-Villanueva <adiez at>, Roberto Malinverni <roberto.malinverni at> and Bernat Gel <bgel at>

Maintainer: Bernat Gel <bgel at>

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


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

regioneR vignette HTML R Script
Reference Manual PDF


biocViews ChIPSeq, CopyNumberVariation, DNASeq, Genetics, MethylSeq, Software
Version 1.36.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License Artistic-2.0
Depends GenomicRanges
Imports memoise, GenomicRanges, IRanges, BSgenome, Biostrings, rtracklayer, parallel, graphics, stats, utils, methods, GenomeInfoDb, S4Vectors, tools
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat
Linking To
Depends On Me karyoploteR, regioneReloaded
Imports Me annotatr, ChIPpeakAnno, CNVfilteR, CopyNumberPlots, karyoploteR, RgnTX, UMI4Cats
Suggests Me CNVRanger, EpiMix, UPDhmm, MitoHEAR
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package regioneR_1.36.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) regioneR_1.36.0.tgz
macOS Binary (arm64) regioneR_1.36.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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