regioneReloaded

This is the development version of regioneReloaded; for the stable release version, see regioneReloaded.

RegioneReloaded: Multiple Association for Genomic Region Sets

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.3.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	Artistic-2.0
Depends	R (>= 4.2), regioneR
Imports	stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2, methods, scales, cluster, grid, grDevices
Linking To
Suggests	rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0)
System Requirements
Enhances
URL	https://github.com/RMalinverni/regioneReload

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	regioneReloaded_1.3.0.tar.gz
Windows Binary	regioneReloaded_1.3.0.zip
macOS Binary (x86_64)	regioneReloaded_1.3.0.tgz
macOS Binary (arm64)	regioneReloaded_1.3.0.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