.plotBubbles	dot-plotBubbles
.prepareNavPage	dot-prepareNavPage
analyseDrugSetEnrichment	analyseDrugSetEnrichment
as.table.referenceComparison	as.table.referenceComparison
calculateCellLineMean	calculateCellLineMean
calculateEvenlyDistributedBins	calculateEvenlyDistributedBins
checkColnames	checkColnames
chunkColumns	chunkColumns
closeOpenHandles	closeOpenHandles
cmapMetadata	cmapMetadata
cmapPerturbationsCompounds	cmapPerturbationsCompounds
cmapPerturbationsKD	cmapPerturbationsKD
compareAgainstCMap	rankSimilarPerturbations
compareQuantile	compareQuantile
compareWithAllMethods	compareWithAllMethods
convertENSEMBLtoGeneSymbols	convertENSEMBLtoGeneSymbols
counts	counts
cTRAP	cTRAP
diffExprStat	diffExprStat
dim.expressionDrugSensitivityAssociation	dimnames.expressionDrugSensitivityAssociation
dim.perturbationChanges	plot.perturbationChanges
dimnames.expressionDrugSensitivityAssociation	dimnames.expressionDrugSensitivityAssociation
dimnames.perturbationChanges	plot.perturbationChanges
downloadENCODEknockdownMetadata	downloadENCODEknockdownMetadata
downloadIfNotFound	downloadIfNotFound
ENCODEmetadata	ENCODEmetadata
filterCMapMetadata	filterCMapMetadata
findIntersectingCompounds	findIntersectingCompounds
fix.datatypes	fix.datatypes
GCT-class	GCT-class
getCMapConditions	getCMapConditions
getCMapPerturbationTypes	getCMapPerturbationTypes
getENCODEcontrols	getENCODEcontrols
HTMLfast	HTMLfast
launchCMapDataLoader	launchCMapDataLoader
launchDiffExprLoader	launchDiffExprLoader
launchDrugSetEnrichmentAnalyser	launchDrugSetEnrichmentAnalyser
launchMetadataViewer	launchMetadataViewer
launchResultPlotter	launchResultPlotter
listExpressionDrugSensitivityAssociation	listExpressionDrugSensitivityAssociation
loadCMapData	loadCMapData
loadCMapZscores	loadCMapZscores
loadCTRPcompoundInfo	loadCTRPgeneExpression
loadCTRPdrugSensitivity	loadCTRPgeneExpression
loadCTRPgeneExpression	loadCTRPgeneExpression
loadDrugDescriptors	loadDrugDescriptors
loadENCODEsample	loadENCODEsample
loadENCODEsamples	loadENCODEsamples
loadExpressionDrugSensitivityAssociation	loadExpressionDrugSensitivityAssociation
loadGDSC7cellLineInfo	loadCTRPgeneExpression
loadGDSC7compoundInfo	loadCTRPgeneExpression
loadGDSC7drugSensitivity	loadCTRPgeneExpression
loadGDSC7file	loadCTRPgeneExpression
loadGDSC7geneExpression	loadCTRPgeneExpression
loadNCI60drugSensitivity	loadNCI60drugSensitivity
loadNCI60geneExpression	loadCTRPgeneExpression
matchStatsWithDrugSetsID	matchStatsWithDrugSetsID
parseCMapID	parseCMapID
performDifferentialExpression	performDifferentialExpression
performGSEA	performGSEA
plot.perturbationChanges	plot.perturbationChanges
plot.referenceComparison	plot.referenceComparison
plotDrugSetEnrichment	plotDrugSetEnrichment
plotESplot	plotESplot
plotGSEA	plotGSEA
plotMetricDistribution	plotMetricDistribution
plotSingleCorr	plotSingleCorr
plotTargetingDrugsVSsimilarPerturbations	plotTargetingDrugsVSsimilarPerturbations
predictTargetingDrugs	predictTargetingDrugs
prepareCMapPerturbations	prepareCMapPerturbations
prepareDrugSets	prepareDrugSets
prepareENCODEgeneExpression	prepareENCODEgeneExpression
prepareExpressionDrugSensitivityAssociation	prepareExpressionDrugSensitivityAssociation
prepareGSEAgenesets	prepareGSEAgenesets
prepareSetsCompoundInfo	prepareSetsCompoundInfo
prepareStatsCompoundInfo	prepareStatsCompoundInfo
prepareWordBreak	prepareWordBreak
print.similarPerturbations	print.similarPerturbations
processByChunks	processByChunks
processIds	processIds
rankAgainstReference	rankAgainstReference
rankColumns	rankColumns
rankSimilarPerturbations	rankSimilarPerturbations
readGctxIds	readGctxIds
readGctxMeta	readGctxMeta
stripStr	stripStr
subsetData	subsetData
subsetDim	subsetDim
subsetToIds	subsetToIds
[.expressionDrugSensitivityAssociation	dimnames.expressionDrugSensitivityAssociation
[.perturbationChanges	plot.perturbationChanges
