regioneR

DOI: 10.18129/B9.bioc.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 (3.8)

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 <rmalinverni at carrerasresearch.org> 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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("regioneR", version = "devel")

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 1.13.2
In Bioconductor since BioC 3.1 (R-3.2) (3.5 years)
License Artistic-2.0
Depends GenomicRanges
Imports memoise, GenomicRanges, IRanges, BSgenome, Biostrings, rtracklayer, parallel, graphics, stats, utils, methods, GenomeInfoDb, S4Vectors
LinkingTo
Suggests BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19.masked, testthat
SystemRequirements
Enhances
URL
Depends On Me karyoploteR
Imports Me annotatr, ChIPpeakAnno, karyoploteR
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package regioneR_1.13.2.tar.gz
Windows Binary regioneR_1.13.2.zip
Mac OS X 10.11 (El Capitan) regioneR_1.13.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/regioneR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/regioneR
Package Short Url http://bioconductor.org/packages/regioneR/
Package Downloads Report Download Stats

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