regioneReloaded
RegioneReloaded: Multiple Association for Genomic Region Sets
Bioconductor version: 3.23 · Package version: 1.14.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("regioneReloaded")Details
| Maintainer | Roberto Malinverni <roberto.malinverni@gmail.com> |
| Author | Roberto Malinverni [aut, cre] (ORCID: <https://orcid.org/0000-0002-0113-3417>), David Corujo [aut], Bernat Gel [aut] |
| License | Artistic-2.0 |
| URL | https://github.com/RMalinverni/regioneReload |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChIPSeq, Clustering, CopyNumberVariation, DNASeq, Genetics, MethylSeq, MultipleComparison, Software |
| Package Short Url | https://bioconductor.org/packages/regioneReloaded/ |
Citation
From within R, enter citation("regioneReloaded"):
Roberto Malinverni, David Corujo, Bernat Gel. regioneReloaded: RegioneReloaded: Multiple Association for Genomic Region Sets. doi:10.18129/B9.bioc.regioneReloaded, R package version 1.14.0, https://bioconductor.org/packages/regioneReloaded.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | regioneReloaded_1.14.0.tar.gz |
| Windows binary (x86_64) | regioneReloaded_1.14.0.zip |
| macOS binary (arm64) | regioneReloaded_1.14.0.tgz |
| macOS binary (x86_64) | regioneReloaded_1.14.0.tgz |
Dependencies
Depends: R (>= 4.2), regioneR
Imports: stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2, methods, scales, cluster, grid, grDevices
Suggests: rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0)