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 (3.21)
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] (ORCID:
Maintainer: Roberto Malinverni <roberto.malinverni at gmail.com>
citation("regioneReloaded")):
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("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 | 1.9.0 |
| 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_1.9.0.tar.gz |
| Windows Binary (x86_64) | regioneReloaded_1.9.0.zip (64-bit only) |
| macOS Binary (x86_64) | regioneReloaded_1.9.0.tgz |
| macOS Binary (arm64) | regioneReloaded_1.9.0.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 |