categoryCompare-package	categoryCompare-package
allAnnotation	ccCompareResult-class
allAnnotation,ccCompareResult-method	ccCompareResult-class
annotation,ccSigList-method	ccSigList-class
breakEdges	breakEdges-methods
breakEdges,ccCompareResult,numeric-method	breakEdges-methods
breakEdges,numeric,numeric-method	breakEdges-methods
breakEdges-methods	breakEdges-methods
category,ccSigList-method	ccSigList-class
category,GENccEnrichResult-method	GENccEnrichResult-class
categoryCompare	categoryCompare-package
ccCompare	ccCompare
ccCompare,ccEnrichCollection,ccOptions-method	ccCompare
ccCompare,GENccEnrichResult,ccOptions-method	ccCompare
ccCompare,GOccEnrichResult,ccOptions-method	ccCompare
ccCompare,KEGGccEnrichResult,ccOptions-method	ccCompare
ccCompare-methods	ccCompare
ccCompareCollection	ccCompareCollection-class
ccCompareCollection-class	ccCompareCollection-class
ccCompareGeneric	ccCompareGeneric-methods
ccCompareGeneric,GENccEnrichResult,ccOptions-method	GENccEnrichResult-class
ccCompareGeneric-methods	ccCompareGeneric-methods
ccCompareResult	ccCompareResult-class
ccCompareResult-class	ccCompareResult-class
ccData	ccData
ccEnrich	ccEnrich
ccEnrich,ccGeneList-method	ccEnrich
ccEnrich-method	ccEnrich
ccEnrichCollection	ccEnrichCollection-class
ccEnrichCollection-class	ccEnrichCollection-class
ccEnrichResult	ccEnrichResult-class
ccEnrichResult-class	ccEnrichResult-class
ccGeneList	ccGeneList-class
ccGeneList-class	ccGeneList-class
ccOptions	ccOptions-class
ccOptions,ccCompareGeneric-method	ccCompareGeneric-methods
ccOptions-class	ccOptions-class
ccOpts	ccData
ccOutCyt	ccOutCyt-methods
ccOutCyt,ccCompareResult,ccOptions-method	ccOutCyt-methods
ccOutCyt-methods	ccOutCyt-methods
ccResults	ccData
ccResultsBPHier	ccData
ccSigList	ccSigList-class
ccSigList-class	ccSigList-class
ccType	ccGeneList-class
ccType,ccGeneList-method	ccGeneList-class
ccType<-	ccGeneList-class
ccType<-,ccGeneList-method	ccGeneList-class
compareColors	ccOptions-class
compareColors,ccOptions-method	ccOptions-class
compareColors<-	ccOptions-class
compareColors<-,ccOptions-method	ccOptions-class
compareIndx	ccOptions-class
compareIndx,ccOptions-method	ccOptions-class
compareNames	ccOptions-class
compareNames,ccOptions-method	ccOptions-class
compareNames<-	ccOptions-class
compareNames<-,ccOptions-method	ccOptions-class
cssClass	ccOptions-class
cssClass,ccOptions-method	ccOptions-class
cwReload	cwReload-methods
cwReload,numeric,ccOptions-method	cwReload-methods
cwReload,numeric,character,ccOptions-method	cwReload-methods
cwReload-methods	cwReload-methods
cytOutData	cytOutData-methods
cytOutData,list,ccCompareResult,mergedData-method	cytOutData-methods
cytOutData,list,ccCompareResult,missing-method	cytOutData-methods
cytOutData,list,missing,missing-method	cytOutData-methods
cytOutData-methods	cytOutData-methods
cytOutNodes	cytOutNodes-methods
cytOutNodes,character,numeric,list-method	cytOutNodes-methods
cytOutNodes,character,numeric,missing-method	cytOutNodes-methods
cytOutNodes-methods	cytOutNodes-methods
enrichLists	ccData
fdr	fdr
fdr,ccEnrichResult-method	ccEnrichResult-class
fdr,ccGeneList-method	ccGeneList-class
fdr,HyperGParamsCC-method	HyperGParamsCC-class
fdr,HyperGResultCC-method	HyperGResultCC-class
fdr<-	fdr
fdr<-,ccGeneList-method	ccGeneList-class
fdr<-,HyperGParamsCC-method	HyperGParamsCC-class
fdrvalues	HyperGResultCC-class
fdrvalues,HyperGResultCC-method	HyperGResultCC-class
fdrvalues-method	HyperGResultCC-class
GENccEnrichResult	GENccEnrichResult-class
GENccEnrichResult,ccCompareGeneric-method	ccCompareGeneric-methods
GENccEnrichResult-class	GENccEnrichResult-class
geneAnnMapping	GENccEnrichResult-class
geneAnnMapping,GENccEnrichResult-method	GENccEnrichResult-class
geneLists	ccData
getAnnotation	getGeneSymbol
getGeneName	getGeneSymbol
getGeneSymbol	getGeneSymbol
getGO2ALLEGS	getGeneSymbol
getPATH2EG	getGeneSymbol
GOccEnrichResult	ccEnrichResult-class
GOccEnrichResult-class	ccEnrichResult-class
GOHyperGParams	HyperGParamsCC-class
GOHyperGParams-class	HyperGParamsCC-class
GOHyperGParamsCC	HyperGParamsCC-class
GOHyperGParamsCC-class	HyperGParamsCC-class
GOHyperGResultCC	HyperGResultCC-class
GOHyperGResultCC-class	HyperGResultCC-class
graphType	graphType-methods
graphType,ccEnrichCollection-method	ccEnrichCollection-class
graphType,ccEnrichResult-method	ccEnrichResult-class
graphType,GENccEnrichResult-method	GENccEnrichResult-class
graphType-methods	graphType-methods
graphType<-	graphType-methods
graphType<-,ccEnrichCollection-method	ccEnrichCollection-class
graphType<-,ccEnrichResult-method	ccEnrichResult-class
graphType<-,GENccEnrichResult-method	GENccEnrichResult-class
gseaRes	ccData
gUniverse	ccData
HyperGParamsCC	HyperGParamsCC-class
HyperGParamsCC-class	HyperGParamsCC-class
HyperGResultCC	HyperGResultCC-class
HyperGResultCC-class	HyperGResultCC-class
hyperGTestCC	hyperGTestCC
hyperGTestCC,HyperGParamsCC	hyperGTestCC
hyperGTestCC,HyperGParamsCC-method	hyperGTestCC
KEGGccEnrichResult	ccEnrichResult-class
KEGGccEnrichResult-class	ccEnrichResult-class
KEGGHyperGParams	HyperGParamsCC-class
KEGGHyperGParams-class	HyperGParamsCC-class
KEGGHyperGParamsCC	HyperGParamsCC-class
KEGGHyperGParamsCC-class	HyperGParamsCC-class
KEGGHyperGResultCC	HyperGResultCC-class
KEGGHyperGResultCC-class	HyperGResultCC-class
listNames	listNames
listNames,ccGeneList-method	ccGeneList-class
listNames,ccOptions-method	ccOptions-class
listNames<-,ccOptions-method	ccOptions-class
mainGraph	ccCompareResult-class
mainGraph,ccCompareResult-method	ccCompareResult-class
mainTable	ccCompareResult-class
mainTable,ccCompareResult-method	ccCompareResult-class
mergedData-class	mergedData-class
mergeLists	mergeLists-methods
mergeLists,ccGeneList,ccOptions-method	mergeLists-methods
mergeLists-methods	mergeLists-methods
minCount	minCount
minCount,ccEnrichResult-method	ccEnrichResult-class
minCount,HyperGResultCC-method	HyperGResultCC-class
minCount<-	minCount
minCount<-,ccEnrichCollection-method	ccEnrichCollection-class
minCount<-,ccEnrichResult-method	ccEnrichResult-class
minCount<-,HyperGResultCC-method	HyperGResultCC-class
minNodes	minNodes
minNodes,CytoscapeWindowClass,numeric-method	minNodes
ontology,ccSigList-method	ccSigList-class
ontology,GENccEnrichResult-method	GENccEnrichResult-class
outType	ccOptions-class
outType,ccOptions-method	ccOptions-class
outType<-	ccOptions-class
outType<-,ccOptions-method	ccOptions-class
pCC,HyperGResultCC-method	HyperGResultCC-class
pvalueCutoff,ccEnrichResult-method	ccEnrichResult-class
pvalueCutoff,ccGeneList-method	ccGeneList-class
pvalueCutoff<-,ccEnrichCollection-method	ccEnrichCollection-class
pvalueCutoff<-,ccEnrichResult-method	ccEnrichResult-class
pvalueCutoff<-,ccGeneList-method	ccGeneList-class
pvalueCutoff<-,HyperGResultCC-method	HyperGResultCC-class
pvalueType	pvalueType
pvalueType,ccEnrichResult-method	ccEnrichResult-class
pvalueType,HyperGResultCC-method	HyperGResultCC-class
pvalueType<-	pvalueType
pvalueType<-,ccEnrichCollection-method	ccEnrichCollection-class
pvalueType<-,ccEnrichResult-method	ccEnrichResult-class
pvalueType<-,HyperGResultCC-method	HyperGResultCC-class
resetColors	resetColors-methods
resetColors,numeric,ccOptions-method	resetColors-methods
resetColors-methods	resetColors-methods
show,HyperGResultCC-method	show-methods
show-methods	show-methods
sigID	GENccEnrichResult-class
sigID,ccSigList-method	ccSigList-class
summary,HyperGResultCC-method	show-methods
summary-methods	show-methods
table10	ccData
table48	ccData
testDirection,ccGeneList-method	ccGeneList-class
[,ccEnrichResult,ANY,ANY,ANY-method	ccEnrichResult-class
[,ccEnrichResult,ANY,ANY-method	ccEnrichResult-class
[,GENccEnrichResult,ANY,ANY,ANY-method	GENccEnrichResult-class
[,GENccEnrichResult,ANY,ANY-method	GENccEnrichResult-class
