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regioneR

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 iconcologia.net>, Roberto Malinverni <roberto.malinverni at gmail.com> and Bernat Gel <bgel at igtp.cat>

Maintainer: Bernat Gel <bgel at imppc.org>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("regioneR")

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

Documentation

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

browseVignettes("regioneR")
regioneR vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

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
URL
See More
Suggests BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat
Linking To
Enhances
Depends On Me karyoploteR, regioneReloaded
Imports Me annotatr, ChIPpeakAnno, CNVfilteR, CopyNumberPlots, karyoploteR, RgnTX, UMI4Cats
Suggests Me CNVRanger, EpiMix, UPDhmm, MitoHEAR
Links To Me
Build Report Build Report

Package Archives

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

Source Package regioneR_1.36.0.tar.gz
Windows Binary regioneR_1.36.0.zip (64-bit only)
macOS Binary (x86_64) regioneR_1.36.0.tgz
macOS Binary (arm64) regioneR_1.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/regioneR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/regioneR
Bioc Package Browser https://code.bioconductor.org/browse/regioneR/
Package Short Url https://bioconductor.org/packages/regioneR/
Package Downloads Report Download Stats