regioneR

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

Association analysis of genomic regions based on permutation tests

Bioconductor version: 3.16

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, CopyNumberVariation, DNASeq, Genetics, MethylSeq, Software

Version 1.30.0

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

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, RIPAT, RLSeq, UMI4Cats

Suggests Me CNVRanger, EpiMix

Links To Me

Build Report Build Report

Package Archives

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

Source Package regioneR_1.30.0.tar.gz

Windows Binary regioneR_1.30.0.zip

macOS Binary (x86_64) regioneR_1.30.0.tgz

macOS Binary (arm64) regioneR_1.30.0.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

Old Source Packages for BioC 3.16 Source Archive