topGO

DOI: 10.18129/B9.bioc.topGO  

Enrichment Analysis for Gene Ontology

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	topGO
PDF		Reference Manual

Details

biocViews	Microarray, Software, Visualization
Version	2.50.0
In Bioconductor since	BioC 2.0 (R-2.5) (16 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
LinkingTo
Suggests	ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest
SystemRequirements
Enhances
URL
Depends On Me	BgeeDB, ccTutorial, cellTree, compEpiTools, EGSEA, ideal, maEndToEnd, moanin, tRanslatome
Imports Me	APL, BioMM, cellity, consICA, ExpHunterSuite, FoldGO, GOSim, GRaNIE, OmaDB, pcaExplorer, psygenet2r, transcriptogramer, ViSEAGO
Suggests Me	FGNet, geva, IntramiRExploreR, miRNAtap, pareg, Ringo
Links To Me
Build Report

Package Archives

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

Source Package	topGO_2.50.0.tar.gz
Windows Binary	topGO_2.50.0.zip
macOS Binary (x86_64)	topGO_2.50.0.tgz
macOS Binary (arm64)	topGO_2.50.0.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