topGO

This is the development version of topGO; for the stable release version, see topGO.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

Enrichment Analysis for Gene Ontology

Bioconductor version: Development (3.24)

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 [aut], Jörg Rahnenführer [aut], Federico Marini [cre] ORCID: 0000-0003-3252-7758

Maintainer: Federico Marini <marinif at uni-mainz.de>

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

Adrian Alexa, Jörg Rahnenführer. topGO: Enrichment Analysis for Gene Ontology. doi:10.18129/B9.bioc.topGO, R package version 2.65.0, https://bioconductor.org/packages/topGO.

Generated from the package metadata; it may differ from the package's own citation.

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("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")

Gene set enrichment analysis with topGO	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, GO, GeneExpression, GeneSetEnrichment, Microarray, Pathways, Sequencing, Software, SystemsBiology, Transcriptomics, Visualization
Version	2.65.0
In Bioconductor since	BioC 2.0 (R-2.5) (19.5 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	https://github.com/federicomarini/topGO
Bug Reports	https://github.com/federicomarini/topGO/issues

Suggests	ALL, hgu95av2.db, hgu133a.db, genefilter, multtest, Rgraphviz, globaltest, knitr, BiocStyle, rmarkdown
Linking To
Enhances
Depends On Me	BgeeDB, compEpiTools, EGSEA, ideal, maEndToEnd, tRanslatome
Imports Me	APL, cellity, consICA, ExpHunterSuite, GRaNIE, mosdef, OmaDB, pcaExplorer, transcriptogramer, ViSEAGO
Suggests Me	DeeDeeExperiment, diffwrap, EMMA, fenr, FGNet, GeDi, geva, IntramiRExploreR, miRNAtap
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	topGO_2.65.0.tar.gz
Windows Binary (x86_64)	topGO_2.65.0.zip
macOS Binary (big-sur-x86_64)	topGO_2.65.0.tgz
macOS Binary (sonoma-arm64)	topGO_2.65.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/topGO
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/topGO
Package Short Url	https://bioconductor.org/packages/topGO/
Package Downloads Report	Download Stats