topGO

topGO: Enrichment analysis for Gene Ontology

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("topGO")

To cite this package in a publication, start R and enter:

    citation("topGO")

Documentation

PDF R Script topGO
PDF   Reference Manual

Details

biocViews Microarray, Software, Visualization
Version 2.16.0
In Bioconductor since BioC 2.0 (R-2.5)
License LGPL
Depends R (>= 2.10.0), methods, graph(>= 1.14.0), Biobase(>= 2.0.0), GO.db(>= 2.3.0), AnnotationDbi(>= 1.7.19), SparseM (>= 0.73)
Imports methods, graph, Biobase, SparseM, AnnotationDbi, lattice
Suggests ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest
System Requirements
URL
Depends On Me ccTutorial, RNAither, tRanslatome
Imports Me GOSim
Suggests Me Ringo

Package Downloads

Package Source topGO_2.16.0.tar.gz
Windows Binary topGO_2.16.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) topGO_2.16.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center