regioneR

DOI: 10.18129/B9.bioc.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>

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")

 

HTML	R Script	regioneR vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, CopyNumberVariation, DNASeq, Genetics, MethylSeq, Software
Version	1.30.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 years)
License	Artistic-2.0
Depends	GenomicRanges
Imports	memoise, GenomicRanges, IRanges, BSgenome, Biostrings, rtracklayer, parallel, graphics, stats, utils, methods, GenomeInfoDb, S4Vectors, tools
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat
SystemRequirements
Enhances
URL
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

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