GOstats

Tools for manipulating GO and microarrays


Bioconductor version: Release (3.20)

A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

Author: Robert Gentleman [aut], Seth Falcon [ctb], Robert Castelo [ctb], Sonali Kumari [ctb] (Converted vignettes from Sweave to R Markdown / HTML.), Dennis Ndubi [ctb] (Converted GOstatsHyperG vignette from Sweave to R Markdown / HTML.), Bioconductor Package Maintainer [cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("GOstats")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GOstats")

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("GOstats")
How To Use GOstats and Category to do Hypergeometric testing with unsupported model organisms HTML R Script
Hypergeometric Tests Using GOstats HTML R Script
Visualizing and Distances Using GO HTML R Script
Reference Manual PDF

Details

biocViews Annotation, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Microarray, MultipleComparison, Pathways, Software
Version 2.72.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19.5 years)
License Artistic-2.0
Depends R (>= 2.10), Biobase(>= 1.15.29), Category(>= 2.43.2), graph
Imports methods, stats, stats4, AnnotationDbi(>= 0.0.89), GO.db(>= 1.13.0), RBGL, annotate(>= 1.13.2), AnnotationForge, Rgraphviz
System Requirements
URL
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Suggests hgu95av2.db(>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr
Linking To
Enhances
Depends On Me MineICA
Imports Me GmicR, SGCP, affycoretools, attract, categoryCompare, ideal, miRLAB, pcaExplorer, scTensor, DNLC
Suggests Me Category, GSEAlm, MLP, MineICA, RnBeads, a4, fastLiquidAssociation, fgga, interactiveDisplay, qpgraph, safe, maGUI, sand
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GOstats_2.72.0.tar.gz
Windows Binary (x86_64) GOstats_2.72.0.zip
macOS Binary (x86_64) GOstats_2.72.0.tgz
macOS Binary (arm64) GOstats_2.71.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GOstats
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GOstats
Bioc Package Browser https://code.bioconductor.org/browse/GOstats/
Package Short Url https://bioconductor.org/packages/GOstats/
Package Downloads Report Download Stats