ALLModules	ALLModules
ALLModulesSmall	ALLModules
annotate	eisa.biclust
annotation,ISAModules-method	ISAModules-class
anrichment	enrichment
CHRListHyperGParams	ListHyperGParams-class
CHRListHyperGParams-class	ListHyperGParams-class
CHRListHyperGResult	ListHyperGResult-class
CHRListHyperGResult-class	ListHyperGResult-class
class:ISAModules	ISAModules-class
coerce,Biclust,ISAModules-method	eisa.biclust
coerce,ISAModules,Biclust-method	eisa.biclust
condGeneIdUniverse,CHRListHyperGResult-method	ListHyperGResult-class
condGeneIdUniverse,GeneralListHyperGResult-method	ListHyperGResult-class
condGeneIdUniverse,GOListHyperGResult-method	ListHyperGResult-class
condGeneIdUniverse,KEGGListHyperGResult-method	ListHyperGResult-class
condGeneIdUniverse,ListHyperGResult-method	ListHyperGResult-class
condGeneIdUniverse,miRNAListHyperGResult-method	ListHyperGResult-class
conditional,GOListHyperGParams-method	ListHyperGParams-class
conditional,GOListHyperGResult-method	ListHyperGResult-class
conditional<-,GOListHyperGParams,logical-method	ListHyperGParams-class
condPlot	cond.plot
dim,ISAModules-method	ISAModules-class
drive	ListHyperGParams-class
drive,CHRListHyperGParams-method	ListHyperGParams-class
drive,GeneralListHyperGParams-method	ListHyperGParams-class
drive,GOListHyperGParams-method	ListHyperGParams-class
drive,KEGGListHyperGParams-method	ListHyperGParams-class
drive,ListHyperGParams-method	ListHyperGParams-class
drive,miRNAListHyperGParams-method	ListHyperGParams-class
drive<-	ListHyperGParams-class
drive<-,CHRListHyperGParams,logical-method	ListHyperGParams-class
drive<-,GeneralListHyperGParams,logical-method	ListHyperGParams-class
drive<-,GOListHyperGParams,logical-method	ListHyperGParams-class
drive<-,KEGGListHyperGParams,logical-method	ListHyperGParams-class
drive<-,ListHyperGParams,logical-method	ListHyperGParams-class
drive<-,miRNAListHyperGParams,logical-method	ListHyperGParams-class
expectedCounts,CHRListHyperGResult-method	ListHyperGResult-class
expectedCounts,GeneralListHyperGResult-method	ListHyperGResult-class
expectedCounts,GOListHyperGResult-method	ListHyperGResult-class
expectedCounts,KEGGListHyperGResult-method	ListHyperGResult-class
expectedCounts,ListHyperGResult-method	ListHyperGResult-class
expectedCounts,miRNAListHyperGResult-method	ListHyperGResult-class
expPlot	exp.plot
expPlotColbar	exp.plot
expPlotCreate	exp.plot
featExprs	ISAExpressionSet
featExprs,ISAExpressionSet-method	ISAExpressionSet
featureNames,ISAModules-method	ISAModules-class
featureThreshold	ISAModules-class
featureThreshold,ISAModules-method	ISAModules-class
geneCounts,CHRListHyperGResult-method	ListHyperGResult-class
geneCounts,GeneralListHyperGResult-method	ListHyperGResult-class
geneCounts,GOListHyperGResult-method	ListHyperGResult-class
geneCounts,KEGGListHyperGResult-method	ListHyperGResult-class
geneCounts,ListHyperGResult-method	ListHyperGResult-class
geneCounts,miRNAListHyperGResult-method	ListHyperGResult-class
geneIdsByCategory,CHRListHyperGResult-method	ListHyperGResult-class
geneIdsByCategory,GeneralListHyperGResult-method	ListHyperGResult-class
geneIdsByCategory,GOListHyperGResult-method	ListHyperGResult-class
geneIdsByCategory,KEGGListHyperGResult-method	ListHyperGResult-class
geneIdsByCategory,ListHyperGResult-method	ListHyperGResult-class
geneIdsByCategory,miRNAListHyperGResult-method	ListHyperGResult-class
geneIdUniverse,CHRListHyperGResult-method	ListHyperGResult-class
geneIdUniverse,GeneralListHyperGResult-method	ListHyperGResult-class
geneIdUniverse,GOListHyperGResult-method	ListHyperGResult-class
geneIdUniverse,KEGGListHyperGResult-method	ListHyperGResult-class
geneIdUniverse,ListHyperGResult-method	ListHyperGResult-class
geneIdUniverse,miRNAListHyperGResult-method	ListHyperGResult-class
geneMappedCount,CHRListHyperGResult-method	ListHyperGResult-class
geneMappedCount,GeneralListHyperGResult-method	ListHyperGResult-class
geneMappedCount,GOListHyperGResult-method	ListHyperGResult-class
geneMappedCount,KEGGListHyperGResult-method	ListHyperGResult-class
geneMappedCount,ListHyperGResult-method	ListHyperGResult-class
geneMappedCount,miRNAListHyperGResult-method	ListHyperGResult-class
GeneralListHyperGParams	ListHyperGParams-class
GeneralListHyperGParams-class	ListHyperGParams-class
GeneralListHyperGResult	ListHyperGResult-class
GeneralListHyperGResult-class	ListHyperGResult-class
getFeatureMatrix	ISAModules-class
getFeatureMatrix,ISAModules-method	ISAModules-class
getFeatureNames	ISAModules-class
getFeatureNames,ISAModules-method	ISAModules-class
getFeatures	ISAModules-class
getFeatures,ISAModules-method	ISAModules-class
getFeatureScores	ISAModules-class
getFeatureScores,ISAModules-method	ISAModules-class
getFullFeatureMatrix	ISAModules-class
getFullFeatureMatrix,ISAModules-method	ISAModules-class
getFullSampleMatrix	ISAModules-class
getFullSampleMatrix,ISAModules-method	ISAModules-class
getNoFeatures	ISAModules-class
getNoFeatures,ISAModules-method	ISAModules-class
getNoSamples	ISAModules-class
getNoSamples,ISAModules-method	ISAModules-class
getOrganism	ISAModules-class
getOrganism,ISAModules-method	ISAModules-class
getSampleMatrix	ISAModules-class
getSampleMatrix,ISAModules-method	ISAModules-class
getSampleNames	ISAModules-class
getSampleNames,ISAModules-method	ISAModules-class
getSamples	ISAModules-class
getSamples,ISAModules-method	ISAModules-class
getSampleScores	ISAModules-class
getSampleScores,ISAModules-method	ISAModules-class
gograph	gograph
gographPlot	gograph
GOListHyperGParams	ListHyperGParams-class
GOListHyperGParams-class	ListHyperGParams-class
GOListHyperGResult	ListHyperGResult-class
GOListHyperGResult-class	ListHyperGResult-class
hasNA	ISAExpressionSet
hasNA,ISAExpressionSet-method	ISAExpressionSet
hasNA<-	ISAExpressionSet
hasNA<-,ISAExpressionSet-method	ISAExpressionSet
htmlReport,CHRListHyperGResult-method	ListHyperGResult-class
htmlReport,GeneralListHyperGResult-method	ListHyperGResult-class
htmlReport,GOListHyperGResult-method	ListHyperGResult-class
htmlReport,KEGGListHyperGResult-method	ListHyperGResult-class
htmlReport,ListHyperGResult-method	ListHyperGResult-class
htmlReport,miRNAListHyperGResult-method	ListHyperGResult-class
hyperGTest,CHRListHyperGParams-method	ListHyperGParams-class
hyperGTest,GeneralListHyperGParams-method	ListHyperGParams-class
hyperGTest,GOListHyperGParams-method	ListHyperGParams-class
hyperGTest,KEGGListHyperGParams-method	ListHyperGParams-class
hyperGTest,ListHyperGParams-method	ListHyperGParams-class
hyperGTest,miRNAListHyperGParams-method	ListHyperGParams-class
ISA	ISA
ISA2heatmap	ISA2heatmap
ISACHR	ISA.CHR
ISAEnrichment	enrichment
ISAExpressionSet	ISAExpressionSet
ISAExpressionSet-class	ISAExpressionSet
ISAFilterRobust	robustness
ISAGO	ISA.GO
ISAHTML	ISA.html
ISAHTMLModules	ISA.html
ISAHTMLTable	ISA.html
ISAIterate	ISA.iterate
ISAKEGG	ISA.KEGG
ISAmiRNA	ISA.miRNA
ISAmnplot	mnplot
ISAModules	ISAModules-class
ISAModules-class	ISAModules-class
ISANormalize	ISA.normalize
ISARobustness	robustness
ISASweep	ISA.sweep
ISASweepGraph	ISA.sweep
ISASweepGraphPlot	ISA.sweep
ISAUnique	ISA.unique
KEGGListHyperGParams	ListHyperGParams-class
KEGGListHyperGParams-class	ListHyperGParams-class
KEGGListHyperGResult	ListHyperGResult-class
KEGGListHyperGResult-class	ListHyperGResult-class
length,ISAModules-method	ISAModules-class
ListHyperGParams	ListHyperGParams-class
ListHyperGParams-class	ListHyperGParams-class
ListHyperGResult	ListHyperGResult-class
ListHyperGResult-class	ListHyperGResult-class
makeValidParams,CHRListHyperGParams-method	ListHyperGParams-class
makeValidParams,GeneralListHyperGParams-method	ListHyperGParams-class
makeValidParams,GOListHyperGParams-method	ListHyperGParams-class
makeValidParams,KEGGListHyperGParams-method	ListHyperGParams-class
makeValidParams,ListHyperGParams-method	ListHyperGParams-class
makeValidParams,miRNAListHyperGParams-method	ListHyperGParams-class
miRNAListHyperGParams	ListHyperGParams-class
miRNAListHyperGParams-class	ListHyperGParams-class
miRNAListHyperGResult	ListHyperGResult-class
miRNAListHyperGResult-class	ListHyperGResult-class
mnplot	mnplot
oddsRatios,CHRListHyperGResult-method	ListHyperGResult-class
oddsRatios,GeneralListHyperGResult-method	ListHyperGResult-class
oddsRatios,GOListHyperGResult-method	ListHyperGResult-class
oddsRatios,KEGGListHyperGResult-method	ListHyperGResult-class
oddsRatios,ListHyperGResult-method	ListHyperGResult-class
oddsRatios,miRNAListHyperGResult-method	ListHyperGResult-class
ontology,GOListHyperGParams-method	ListHyperGParams-class
ontology,GOListHyperGResult-method	ListHyperGResult-class
ontology<-,GOListHyperGParams,character-method	ListHyperGParams-class
overlap	overlap
overlapPlot	overlap
pData,ISAModules-method	ISAModules-class
prenormalized	ISAExpressionSet
prenormalized,ISAExpressionSet-method	ISAExpressionSet
prenormalized<-	ISAExpressionSet
prenormalized<-,ISAExpressionSet-method	ISAExpressionSet
print.ISAexpPlot	exp.plot
profilePlot	profilePlot
pvalues,CHRListHyperGResult-method	ListHyperGResult-class
pvalues,GeneralListHyperGResult-method	ListHyperGResult-class
pvalues,GOListHyperGResult-method	ListHyperGResult-class
pvalues,KEGGListHyperGResult-method	ListHyperGResult-class
pvalues,ListHyperGResult-method	ListHyperGResult-class
pvalues,miRNAListHyperGResult-method	ListHyperGResult-class
runData	ISAModules-class
runData,ISAModules-method	ISAModules-class
sampExprs	ISAExpressionSet
sampExprs,ISAExpressionSet-method	ISAExpressionSet
sampleNames,ISAModules-method	ISAModules-class
sampleThreshold	ISAModules-class
sampleThreshold,ISAModules-method	ISAModules-class
seedData	ISAModules-class
seedData,ISAModules-method	ISAModules-class
sigCategories,CHRListHyperGResult-method	ListHyperGResult-class
sigCategories,GeneralListHyperGResult-method	ListHyperGResult-class
sigCategories,GOListHyperGResult-method	ListHyperGResult-class
sigCategories,KEGGListHyperGResult-method	ListHyperGResult-class
sigCategories,ListHyperGResult-method	ListHyperGResult-class
sigCategories,miRNAListHyperGResult-method	ListHyperGResult-class
summary,CHRListHyperGResult-method	ListHyperGResult-class
summary,GeneralListHyperGResult-method	ListHyperGResult-class
summary,GOListHyperGResult-method	ListHyperGResult-class
summary,KEGGListHyperGResult-method	ListHyperGResult-class
summary,ListHyperGResult-method	ListHyperGResult-class
summary,miRNAListHyperGResult-method	ListHyperGResult-class
universeCounts,CHRListHyperGResult-method	ListHyperGResult-class
universeCounts,GeneralListHyperGResult-method	ListHyperGResult-class
universeCounts,GOListHyperGResult-method	ListHyperGResult-class
universeCounts,KEGGListHyperGResult-method	ListHyperGResult-class
universeCounts,ListHyperGResult-method	ListHyperGResult-class
universeCounts,miRNAListHyperGResult-method	ListHyperGResult-class
universeMappedCount,CHRListHyperGResult-method	ListHyperGResult-class
universeMappedCount,GeneralListHyperGResult-method	ListHyperGResult-class
universeMappedCount,GOListHyperGResult-method	ListHyperGResult-class
universeMappedCount,KEGGListHyperGResult-method	ListHyperGResult-class
universeMappedCount,ListHyperGResult-method	ListHyperGResult-class
universeMappedCount,miRNAListHyperGResult-method	ListHyperGResult-class
[,ISAModules,ANY,ANY,ANY-method	ISAModules-class
[,ISAModules,ANY,ANY-method	ISAModules-class
[,ISAModules,ANY-method	ISAModules-class
[[,ISAModules,ANY,ANY-method	ISAModules-class
[[,ISAModules,ANY-method	ISAModules-class
