topGO

topGO: Enrichment analysis for Gene Ontology

Bioconductor version: 2.8

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 <alexa at mpi-inf.mpg.de>

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 topGO_classes_v3.pdf
PDF   Reference Manual

Details

biocViews Microarray, Bioinformatics, Visualization
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
License LGPL
URL
Depends On Me RNAither
Imports Me
Suggests Me Ringo
Version 2.4.0
Since Bioconductor 2.0 (R-2.5)

Package Downloads

Package Source topGO_2.4.0.tar.gz
Windows Binary topGO_2.4.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary topGO_2.4.0.tgz
Package Downloads Report Download Stats

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