topGO

Enrichment Analysis for Gene Ontology

Bioconductor version: 3.24 · Package version: 2.65.0

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.

Installation

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

BiocManager::install("topGO")

Details

Maintainer	Federico Marini <marinif@uni-mainz.de>
Author	Adrian Alexa [aut], Jörg Rahnenführer [aut], Federico Marini [cre] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
License	LGPL
URL	https://github.com/federicomarini/topGO
Bug Reports	https://github.com/federicomarini/topGO/issues
Downloads rank	2875
Source branch	devel
biocViews	Annotation, GO, GeneExpression, GeneSetEnrichment, Microarray, Pathways, Sequencing, Software, SystemsBiology, Transcriptomics, Visualization

Documentation

Gene set enrichment analysis with topGO

Download

Follow the 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 (arm64)	topGO_2.65.0.tgz
macOS binary (x86_64)	topGO_2.65.0.tgz

Dependencies

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

Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, multtest, Rgraphviz, globaltest, knitr, BiocStyle, rmarkdown

Reverse dependencies

Depends On Me (6): BgeeDB, compEpiTools, EGSEA, ideal, maEndToEnd, tRanslatome

Imports Me (10): APL, cellity, consICA, ExpHunterSuite, GRaNIE, mosdef, OmaDB, pcaExplorer, transcriptogramer, ViSEAGO

Suggests Me (9): DeeDeeExperiment, diffwrap, EMMA, fenr, FGNet, GeDi, geva, IntramiRExploreR, miRNAtap