regioneR

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

Association analysis of genomic regions based on permutation tests

Bioconductor version: Development (3.21)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.39.0
In Bioconductor since	BioC 3.1 (R-3.2) (9.5 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	CNVfilteR, ChIPpeakAnno, CopyNumberPlots, RgnTX, UMI4Cats, annotatr, karyoploteR
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_1.39.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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