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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("topGO")
AuthorAdrian Alexa, Jorg Rahnenfuhrer
Bioconductor views Microarray Visualization
Date of publicationNone
MaintainerAdrian Alexa <adrian.alexa@gmail.com>
LicenseLGPL
Version2.26.0

View on Bioconductor

Functions

affyLib Man page
algorithm Man page
algorithm<- Man page
algorithm<-,topGOresult-method Man page
algorithm,topGOresult-method Man page
allGenes Man page
allGenes,topGOdata-method Man page
allMembers Man page
allMembers<- Man page
allMembers<-,classicExpr-method Man page
allMembers,elimScore-method Man page
allMembers<-,groupStats-method Man page
allMembers,groupStats-method Man page
allMembers<-,parentChild-method Man page
allMembers,parentChild-method Man page
allMembers<-,pC-method Man page
allMembers,weight01Expr-method Man page
allMembers,weight01Score-method Man page
allMembers,weightCount-method Man page
allParents Man page
allParents,parentChild-method Man page
allScore Man page
allScore,classicScore,logical-method Man page
allScore,classicScore,missing-method Man page
allScore,elimScore,logical-method Man page
allScore,elimScore,missing-method Man page
allScore,weight01Score,logical-method Man page
allScore,weight01Score,missing-method Man page
alternative,elimScore-method Man page
annFUN Man page
annFUN.db Man page
annFUN.file Man page
annFUN.gene2GO Man page
annFUN.GO2genes Man page
annFUN.org Man page
attrInTerm Man page
attrInTerm,topGOdata,character,character-method Man page
attrInTerm,topGOdata,character,missing-method Man page
buildLevels Man page
classicCount-class Man page
classicExpr-class Man page
classicScore-class Man page
combineResults Man page
contTable Man page
contTable,classicCount-method Man page
contTable,elimCount-method Man page
countGenesInTerm Man page
countGenesInTerm,topGOdata,character-method Man page
countGenesInTerm,topGOdata,missing-method Man page
cutOff Man page
cutOff<- Man page
cutOff<-,elimCount-method Man page
cutOff,elimCount-method Man page
cutOff<-,elimExpr-method Man page
cutOff,elimExpr-method Man page
cutOff<-,elimScore-method Man page
cutOff,elimScore-method Man page
depth Man page
depth<- Man page
depth<-,leaCount-method Man page
depth,leaCount-method Man page
depth<-,leaExpr-method Man page
depth,leaExpr-method Man page
depth<-,leaScore-method Man page
depth,leaScore-method Man page
description Man page
description<- Man page
description<-,topGOdata,ANY-method Man page
description,topGOdata-method Man page
description<-,topGOresult,ANY-method Man page
description,topGOresult-method Man page
elim Man page
elim<- Man page
elimCount-class Man page
elim<-,elimCount-method Man page
elim,elimCount-method Man page
elim<-,elimScore-method Man page
elim,elimScore-method Man page
elimExpr-class Man page
elimScore-class Man page
elim<-,weight01Count-method Man page
elim,weight01Count-method Man page
elim<-,weight01Expr-method Man page
elim,weight01Expr-method Man page
elim<-,weight01Score-method Man page
elim,weight01Score-method Man page
emptyExpr,classicExpr-method Man page
expressionMatrix Man page
expressionMatrix,topGOdata-method Man page
feasible Man page
feasible<- Man page
feasible<-,topGOdata-method Man page
feasible,topGOdata-method Man page
geneData Man page
geneData<- Man page
geneData<-,topGOresult-method Man page
geneData,topGOresult-method Man page
geneList Man page
genes Man page
geneScore Man page
geneScore,topGOdata,character-method Man page
geneScore,topGOdata-method Man page
geneScore,topGOdata,missing-method Man page
geneSelectionFun Man page
geneSelectionFun<- Man page
geneSelectionFun<-,topGOdata-method Man page
geneSelectionFun,topGOdata-method Man page
genesInTerm Man page
genesInTerm,topGOdata,character-method Man page
genesInTerm,topGOdata,missing-method Man page
genes,topGOdata-method Man page
GenTable Man page
GenTable,topGOdata-method Man page
getGraphRoot Man page
getNoOfLevels Man page
getPvalues Man page
getSigGroups Man page
getSigGroups-methods Man page
getSigGroups,topGOdata,classicCount-method Man page
getSigGroups,topGOdata,classicExpr-method Man page
getSigGroups,topGOdata,classicScore-method Man page
getSigGroups,topGOdata,elimCount-method Man page
getSigGroups,topGOdata,elimExpr-method Man page
getSigGroups,topGOdata,elimScore-method Man page
getSigGroups,topGOdata,leaCount-method Man page
getSigGroups,topGOdata,leaExpr-method Man page
getSigGroups,topGOdata,leaScore-method Man page
getSigGroups,topGOdata,parentChild-method Man page
getSigGroups,topGOdata,pC-method Man page
getSigGroups,topGOdata,weight01Count-method Man page
getSigGroups,topGOdata,weight01Expr-method Man page
getSigGroups,topGOdata,weight01Score-method Man page
getSigGroups,topGOdata,weightCount-method Man page
getSigRatio Man page
getSigRatio,weightCount-method Man page
GOBPTerm Man page
GOCCTerm Man page
GOdata Man page
GOFisherTest Man page
GOFisherTest,classicCount-method Man page
GOFisherTest,elimCount-method Man page
GOglobalTest Man page
GOglobalTest,classicExpr-method Man page
GOKSTest Man page
GOKSTest,classicScore-method Man page
GOKSTiesTest Man page
GOKSTiesTest,classicScore-method Man page
GOMFTerm Man page
GOplot Man page
GOSumTest Man page
GOSumTest,classicScore-method Man page
GOtTest Man page
GOtTest,classicScore-method Man page
graph Man page
graph<- Man page
graph<-,topGOdata-method Man page
graph,topGOdata-method Man page
groupGOTerms Man page
groupStats-class Man page
inducedGraph Man page
initialize,classicCount-method Man page
initialize,classicExpr-method Man page
initialize,classicScore-method Man page
initialize,elimCount-method Man page
initialize,elimExpr-method Man page
initialize,elimScore-method Man page
initialize,groupStats-method Man page
initialize,leaCount-method Man page
initialize,leaExpr-method Man page
initialize,leaScore-method Man page
initialize,parentChild-method Man page
initialize,pC-method Man page
initialize,topGOdata-method Man page
initialize,topGOresult-method Man page
initialize,weight01Count-method Man page
initialize,weight01Expr-method Man page
initialize,weight01Score-method Man page
initialize,weightCount-method Man page
inverseList Man page
joinFun Man page
joinFun,parentChild-method Man page
leaCount-class Man page
leaExpr-class Man page
leaScore-class Man page
members Man page
members<- Man page
members,elimScore-method Man page
membersExpr Man page
membersExpr,classicExpr-method Man page
members<-,groupStats-method Man page
members,groupStats,missing-method Man page
membersScore Man page
membersScore,classicScore-method Man page
membersScore,elimScore-method Man page
membersScore,weight01Score-method Man page
members,weight01Expr,missing-method Man page
members,weight01Score,missing-method Man page
members,weightCount-method Man page
Name Man page
Name<- Man page
Name<-,groupStats-method Man page
Name,groupStats-method Man page
Name,weightCount-method Man page
nodesInInducedGraph Man page
numAllMembers Man page
numAllMembers,elimCount-method Man page
numAllMembers,elimScore-method Man page
numAllMembers,groupStats-method Man page
numAllMembers,parentChild-method Man page
numAllMembers,weight01Count-method Man page
numAllMembers,weight01Expr-method Man page
numAllMembers,weight01Score-method Man page
numAllMembers,weightCount-method Man page
numGenes Man page
numGenes,topGOdata-method Man page
numMembers Man page
numMembers,elimCount-method Man page
numMembers,elimScore-method Man page
numMembers,groupStats-method Man page
numMembers,weight01Count-method Man page
numMembers,weight01Expr-method Man page
numMembers,weight01Score-method Man page
numMembers,weightCount-method Man page
numSigAll Man page
numSigAll,classicCount-method Man page
numSigAll,elimCount-method Man page
numSigAll,parentChild-method Man page
numSigAll,weight01Count-method Man page
numSigAll,weightCount-method Man page
numSigGenes Man page
numSigGenes,topGOdata-method Man page
numSigMembers Man page
numSigMembers,classicCount-method Man page
numSigMembers,elimCount-method Man page
numSigMembers,weight01Count-method Man page
numSigMembers,weightCount-method Man page
ontology Man page
ontology<- Man page
ontology<-,topGOdata-method Man page
ontology,topGOdata-method Man page
parentChild-class Man page
pC-class Man page
penalise Man page
penalise,weightCount,numeric,numeric-method Man page
permSumStats Man page
permSumStats.all Man page
phenotype Man page
phenotype,topGOdata-method Man page
printGenes Man page
printGenes-methods Man page
printGenes,topGOdata,character,character-method Man page
printGenes,topGOdata,character,missing-method Man page
printGraph Man page
printGraph-methods Man page
printGraph,topGOdata,topGOresult,numeric,missing-method Man page
printGraph,topGOdata,topGOresult,numeric,topGOresult-method Man page
print,topGOdata-method Man page
print,topGOresult-method Man page
pType Man page
pType<- Man page
pType<-,classicExpr-method Man page
pType,classicExpr-method Man page
rankMembers Man page
rankMembers,classicScore-method Man page
rankMembers,elimScore-method Man page
rankMembers,weight01Score-method Man page
readMappings Man page
resultFisher Man page
resultKS Man page
reverseArch Man page
roundFun Man page
roundFun,weightCount-method Man page
runTest Man page
runTest,groupStats-method Man page
runTest,groupStats,missing,missing-method Man page
runTest,topGOdata,character,character-method Man page
runTest,topGOdata,missing,character-method Man page
score Man page
score<- Man page
score<-,classicScore-method Man page
score<-,elimScore-method Man page
scoreOrder Man page
scoreOrder,classicScore-method Man page
scoresInTerm Man page
scoresInTerm,topGOdata,character-method Man page
scoresInTerm,topGOdata,missing-method Man page
score<-,topGOresult-method Man page
score,topGOresult-method Man page
showGroupDensity Man page
showSigOfNodes Man page
show,topGOdata-method Man page
show,topGOresult-method Man page
sigAllMembers Man page
sigAllMembers,classicCount-method Man page
sigAllMembers,elimCount-method Man page
sigAllMembers,parentChild-method Man page
sigAllMembers,weight01Count-method Man page
sigGenes Man page
sigGenes,topGOdata-method Man page
sigMembers Man page
sigMembers<- Man page
sigMembers<-,classicCount-method Man page
sigMembers,classicCount-method Man page
sigMembers<-,elimCount-method Man page
sigMembers,elimCount-method Man page
sigMembers<-,parentChild-method Man page
sigMembers<-,pC-method Man page
sigMembers,weight01Count-method Man page
significant Man page
significant,weightCount-method Man page
sigRatio Man page
sigRatio<- Man page
sigRatio<-,weightCount-method Man page
sigRatio,weightCount-method Man page
termStat Man page
termStat,topGOdata,character-method Man page
termStat,topGOdata,missing-method Man page
testName Man page
testName<- Man page
testName<-,topGOresult-method Man page
testName,topGOresult-method Man page
testStatistic Man page
testStatistic,groupStats-method Man page
testStatistic,weightCount-method Man page
testStatPar Man page
testStatPar,groupStats-method Man page
testStatPar,weightCount-method Man page
topDiffGenes Man page
topGO Man page
topGOdata-class Man page
topGO-package Man page
topGOresult-class Man page
updateGenes Man page
updateGenes,topGOdata,factor,missing-method Man page
updateGenes,topGOdata,numeric,function-method Man page
updateGroup Man page
updateGroup,groupStats,character,character-method Man page
updateGroup,parentChild,missing,character-method Man page
updateGroup,pC,missing,character-method Man page
updateGroup,pC,missing,missing-method Man page
updateGroup,weightCount,character,character-method Man page
updateTerm<- Man page
updateTerm<-,topGOdata,character-method Man page
usedGO Man page
usedGO,topGOdata-method Man page
weight01Count-class Man page
weight01Expr-class Man page
weight01Score-class Man page
weightCount-class Man page
Weights Man page
Weights<- Man page
Weights,weightCount,logical-method Man page
Weights<-,weightCount-method Man page
Weights,weightCount-method Man page
Weights,weightCount,missing-method Man page
whichAlgorithms Man page
whichTests Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.