topGO: Enrichment Analysis for Gene Ontology

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
Date of publication
None
Maintainer
Adrian Alexa <adrian.alexa@gmail.com>
License
LGPL
Version
2.26.0

View on Bioconductor

Man pages

annFUN
Functions which map gene identifiers to GO terms
classicCount-class
Class "classicCount"
classicExpr-class
Class "classicExpr"
classicScore-class
Class "classicScore"
dagFunctions
Utility functions to work with Directed Acyclic Graphs (DAG)
diagnosticMethods
Diagnostic functions for topGOdata and topGOresult objects.
elimCount-class
Classes "elimCount" and "weight01Count"
elimExpr-class
Class "elimExpr"
elimScore-class
Classes "elimScore" and "weight01Score"
geneList
A toy example of a list of gene identifiers and the...
getPvalues
Convenient function to compute p-values from a gene...
getSigGroups
Interfaces for running the enrichment tests
GOdata
Sample topGOdata and topGOresult objects
GOTests
Gene set tests statistics
groupGOTerms
Grouping of GO terms into the three ontologies
groupStats-class
Class "groupStats"
inducedGraph
The subgraph induced by a set of nodes.
parentChild-class
Classes "parentChild" and "pC"
printGraph-methods
Visualisation functions
topGOdata-class
Class "topGOdata"
topGO-package
Enrichment analysis for Gene Ontology
topGOresult-class
Class "topGOresult"
weightCount-class
Class "weightCount"

Files in this package

topGO/DESCRIPTION
topGO/NAMESPACE
topGO/R
topGO/R/AllClasses.R
topGO/R/topGOalgo.R
topGO/R/topGOannotations.R
topGO/R/topGOfunctions.R
topGO/R/topGOgraph.R
topGO/R/topGOmethods.R
topGO/R/topGOtests.R
topGO/R/topGOviz.R
topGO/R/zzz.R
topGO/build
topGO/build/vignette.rds
topGO/data
topGO/data/GOdata.rda
topGO/data/geneList.rda
topGO/data/results.tGO.rda
topGO/inst
topGO/inst/doc
topGO/inst/doc/topGO.R
topGO/inst/doc/topGO.Rnw
topGO/inst/doc/topGO.pdf
topGO/inst/examples
topGO/inst/examples/geneid2go.map
topGO/inst/scripts
topGO/inst/scripts/GO_ALL.R
topGO/inst/scripts/geneToGOscript.R
topGO/man
topGO/man/GOTests.Rd
topGO/man/GOdata.Rd
topGO/man/annFUN.Rd
topGO/man/classicCount-class.Rd
topGO/man/classicExpr-class.Rd
topGO/man/classicScore-class.Rd
topGO/man/dagFunctions.Rd
topGO/man/diagnosticMethods.Rd
topGO/man/elimCount-class.Rd
topGO/man/elimExpr-class.Rd
topGO/man/elimScore-class.Rd
topGO/man/geneList.Rd
topGO/man/getPvalues.Rd
topGO/man/getSigGroups.Rd
topGO/man/groupGOTerms.Rd
topGO/man/groupStats-class.Rd
topGO/man/inducedGraph.Rd
topGO/man/parentChild-class.Rd
topGO/man/printGraph-methods.Rd
topGO/man/topGO-package.Rd
topGO/man/topGOdata-class.Rd
topGO/man/topGOresult-class.Rd
topGO/man/weightCount-class.Rd
topGO/vignettes
topGO/vignettes/green_ckmark.png
topGO/vignettes/red_ckmark.png
topGO/vignettes/ref_books.bib
topGO/vignettes/topGO.Rnw
topGO/vignettes/topGO_classes_v3.pdf