GSRI
This is the development version of GSRI; for the stable release version, see GSRI.
Gene Set Regulation Index
Bioconductor version: Development (3.24)
The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI).
Author: Julian Gehring, Kilian Bartholome, Clemens Kreutz, Jens Timmer
Maintainer: Julian Gehring <jg-bioc at gmx.com>
citation("GSRI")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GSRI")
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("GSRI")| Introduction to the GSRI package: Estimating Regulatory Effects utilizing the Gene Set Regulation Index | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneRegulation, GeneSetEnrichment, Microarray, Software, Transcription |
| Version | 2.61.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (16.5 years) |
| License | GPL-3 |
| Depends | R (>= 2.14.2), fdrtool |
| Imports | methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les(>= 1.1.6) |
| System Requirements | |
| URL |
See More
| Suggests | limma, hgu95av2.db |
| Linking To | |
| Enhances | parallel |
| 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 | GSRI_2.61.0.tar.gz |
| Windows Binary (x86_64) | GSRI_2.61.0.zip |
| macOS Binary (big-sur-x86_64) | GSRI_2.61.0.tgz |
| macOS Binary (sonoma-arm64) | GSRI_2.61.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GSRI |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GSRI |
| Bioc Package Browser | https://code.bioconductor.org/browse/GSRI/ |
| Package Short Url | https://bioconductor.org/packages/GSRI/ |
| Package Downloads Report | Download Stats |