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("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 | ||
| NEWS | Text |
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 |
See More
| 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 |