regioneR

DOI: 10.18129/B9.bioc.regioneR    

Association analysis of genomic regions based on permutation tests

Bioconductor version: Release (3.6)

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 imppc.org>, Roberto Malinverni <rmalinverni at carrerasresearch.org> and Bernat Gel <bgel at imppc.org>

Maintainer: Bernat Gel <bgel at imppc.org>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("regioneR")

Documentation

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

browseVignettes("regioneR")

 

PDF	R Script	regioneR vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, CopyNumberVariation, DNASeq, Genetics, MethylSeq, Software
Version	1.10.0
In Bioconductor since	BioC 3.1 (R-3.2) (3 years)
License	Artistic-2.0
Depends	memoise, GenomicRanges, BSgenome, rtracklayer, parallel
Imports	memoise, GenomicRanges, BSgenome, rtracklayer, parallel, graphics, stats, utils, methods, GenomeInfoDb, IRanges, 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
Build Report

Package Archives

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

Source Package	regioneR_1.10.0.tar.gz
Windows Binary	regioneR_1.10.0.zip
Mac OS X 10.11 (El Capitan)	regioneR_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/regioneR
Package Short Url	http://bioconductor.org/packages/regioneR/
Package Downloads Report	Download Stats