topGO

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see topGO.

Enrichment Analysis for Gene Ontology

Bioconductor version: 3.21

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Microarray, Software, Visualization

Version 2.60.1

In Bioconductor since BioC 2.0 (R-2.5) (18.5 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

Suggests ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest

Linking To

Enhances

Depends On Me BgeeDB, compEpiTools, EGSEA, ideal, moanin, tRanslatome, maEndToEnd

Imports Me APL, cellity, consICA, GRaNIE, mosdef, OmaDB, pcaExplorer, transcriptogramer, ViSEAGO, ExpHunterSuite

Suggests Me fenr, FGNet, GeDi, geva, IntramiRExploreR, miRNAtap

Links To Me

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