regioneReloaded
RegioneReloaded: Multiple Association for Genomic Region Sets
Bioconductor version: Release (3.19)
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("regioneReloaded")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | ChIPSeq, Clustering, CopyNumberVariation, DNASeq, Genetics, MethylSeq, MultipleComparison, Software |
Version | 1.6.0 |
In Bioconductor since | BioC 3.16 (R-4.2) (2 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_1.6.0.tar.gz |
Windows Binary | regioneReloaded_1.6.0.zip |
macOS Binary (x86_64) | regioneReloaded_1.6.0.tgz |
macOS Binary (arm64) | regioneReloaded_1.6.0.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 |