regioneReloaded
This is the released version of regioneReloaded; for the devel version, see regioneReloaded.
RegioneReloaded: Multiple Association for Genomic Region Sets
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | regioneReloaded_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | regioneReloaded_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | regioneReloaded_1.14.0.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 |