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regioneReloaded

RegioneReloaded: Multiple Association for Genomic Region Sets


Bioconductor version: Release (3.18)

RegioneReloaded is a package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and the creation of ready-to-publish graphs. It takes over and expands on all the features of its predecessor regioneR. It also incorporates a strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. RegioneReloaded builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.

Author: Roberto Malinverni [aut, cre] , David Corujo [aut], Bernat Gel [aut]

Maintainer: Roberto Malinverni <roberto.malinverni at gmail.com>

Citation (from within R, enter citation("regioneReloaded")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("regioneReloaded")

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("regioneReloaded")
regioneReloaded HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Clustering, CopyNumberVariation, DNASeq, Genetics, MethylSeq, MultipleComparison, Software
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2), regioneR
Imports stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2, methods, scales, cluster, grid, grDevices
System Requirements
URL https://github.com/RMalinverni/regioneReload
See More
Suggests rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package regioneReloaded_1.4.0.tar.gz
Windows Binary regioneReloaded_1.4.0.zip (64-bit only)
macOS Binary (x86_64) regioneReloaded_1.4.0.tgz
macOS Binary (arm64) regioneReloaded_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/regioneReloaded
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/regioneReloaded
Bioc Package Browser https://code.bioconductor.org/browse/regioneReloaded/
Package Short Url https://bioconductor.org/packages/regioneReloaded/
Package Downloads Report Download Stats