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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/regioneR.html below:

Bioconductor - regioneR (development version)

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 (3.22)

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")
Details biocViews ChIPSeq, CopyNumberVariation, DNASeq, Genetics, MethylSeq, Software Version 1.41.3 In Bioconductor since BioC 3.1 (R-3.2) (10 years) License Artistic-2.0 Depends GenomicRanges Imports memoise, GenomicRanges, IRanges, BSgenome, Biostrings, rtracklayer, parallel, graphics, stats, utils, methods, Seqinfo, 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, UMI4Cats 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.

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