GSReg
This is the released version of GSReg; for the devel version, see GSReg.
Gene Set Regulation (GS-Reg)
Bioconductor version: Release (3.23)
A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).
Author: Bahman Afsari <bahman at jhu.edu>, Elana J. Fertig <ejfertig at jhmi.edu>
Maintainer: Bahman Afsari <bahman at jhu.edu>, Elana J. Fertig <ejfertig at jhmi.edu>
citation("GSReg")):
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("GSReg")
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("GSReg")| Working with the GSReg package | R Script | |
| Reference Manual |
Details
| biocViews | AlternativeSplicing, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneticVariability, Pathways, Software |
| Version | 1.46.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | GPL-2 |
| Depends | R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | GenomicRanges, GSBenchMark |
| 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 | GSReg_1.46.0.tar.gz |
| Windows Binary (x86_64) | GSReg_1.46.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | GSReg_1.46.0.tgz |
| macOS Binary (sonoma-arm64) | GSReg_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GSReg |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GSReg |
| Bioc Package Browser | https://code.bioconductor.org/browse/GSReg/ |
| Package Short Url | https://bioconductor.org/packages/GSReg/ |
| Package Downloads Report | Download Stats |