mgsa
This is the released version of mgsa; for the devel version, see mgsa.
Model-based gene set analysis
Bioconductor version: Release (3.23)
Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.
Author: Sebastian Bauer <mail at sebastianbauer.info>, Julien Gagneur <gagneur at genzentrum.lmu.de>
Maintainer: Sebastian Bauer <mail at sebastianbauer.info>
citation("mgsa")):
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("mgsa")
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("mgsa")| Overview of the mgsa package. | R Script | |
| Reference Manual |
Details
| biocViews | GO, GeneSetEnrichment, Pathways, Software |
| Version | 1.60.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (15.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.14.0), methods, gplots |
| Imports | graphics, stats, utils |
| System Requirements | |
| URL | https://github.com/sba1/mgsa-bioc |
See More
| Suggests | DBI, RSQLite, GO.db, testthat |
| 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 | mgsa_1.60.0.tar.gz |
| Windows Binary (x86_64) | mgsa_1.60.0.zip |
| macOS Binary (big-sur-x86_64) | mgsa_1.60.0.tgz |
| macOS Binary (sonoma-arm64) | mgsa_1.60.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mgsa |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mgsa |
| Bioc Package Browser | https://code.bioconductor.org/browse/mgsa/ |
| Package Short Url | https://bioconductor.org/packages/mgsa/ |
| Package Downloads Report | Download Stats |