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topGO

Enrichment Analysis for Gene Ontology


Bioconductor version: Release (3.18)

topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Author: Adrian Alexa, Jorg Rahnenfuhrer

Maintainer: Adrian Alexa <adrian.alexa at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("topGO")

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("topGO")
topGO PDF R Script
Reference Manual PDF

Details

biocViews Microarray, Software, Visualization
Version 2.54.0
In Bioconductor since BioC 2.0 (R-2.5) (17 years)
License LGPL
Depends R (>= 2.10.0), methods, BiocGenerics(>= 0.13.6), graph(>= 1.14.0), Biobase(>= 2.0.0), GO.db(>= 2.3.0), AnnotationDbi(>= 1.7.19), SparseM (>= 0.73)
Imports lattice, matrixStats, DBI
System Requirements
URL
See More
Suggests ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest
Linking To
Enhances
Depends On Me BgeeDB, ccTutorial, compEpiTools, EGSEA, ideal, maEndToEnd, moanin, tRanslatome
Imports Me APL, BioMM, cellity, consICA, ExpHunterSuite, FoldGO, GOSim, GRaNIE, OmaDB, pcaExplorer, psygenet2r, transcriptogramer, ViSEAGO
Suggests Me fenr, FGNet, geva, IntramiRExploreR, miRNAtap, pareg, Ringo
Links To Me
Build Report Build Report

Package Archives

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

Source Package topGO_2.54.0.tar.gz
Windows Binary topGO_2.54.0.zip
macOS Binary (x86_64) topGO_2.54.0.tgz
macOS Binary (arm64) topGO_2.54.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/topGO
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/topGO
Bioc Package Browser https://code.bioconductor.org/browse/topGO/
Package Short Url https://bioconductor.org/packages/topGO/
Package Downloads Report Download Stats