.onAttach	dot-onAttach
addObjectAttrs	addObjectAttrs
addTCGAdata	addTCGAdata
analysesPlotSet	analysesTableSet
analysesServer	appServer
analysesTableSet	analysesTableSet
analysesUI	appUI
appendNewGroups	appendNewGroups
appServer	appServer
appUI	appUI
areSplicingEvents	areSplicingEvents
articleUI	articleUI
as.table.GEandAScorrelation	plot.GEandAScorrelation
ASquantFileInput	geneExprFileInput
assignColours	assignColours
assignValuePerPatient	assignValuePerSubject
assignValuePerSubject	assignValuePerSubject
basicStats	basicStats
blendColours	blendColours
browseDownloadFolderInput	browseDownloadFolderInput
browserHistory	browserHistory
calculateInclusionLevels	calculateInclusionLevels
calculateLoadingsContribution	calculateLoadingsContribution
checkFileFormat	checkFileFormat
checkFirebrowse	checkFirebrowse
checkGroupType	checkGroupType
checkIntegrity	checkIntegrity
checkSurvivalInput	checkSurvivalInput
closeProgress	startProgress
clusterICAset	clusterICAset
clusterSet	clusterSet
colourInputMod	colourInputMod
colSums,EList-method	colSums-EList-method
convertGeneIdentifiers	convertGeneIdentifiers
correlateGEandAS	correlateGEandAS
correlationServer	appServer
correlationUI	appUI
createDataTab	createDataTab
createDensitySparklines	createDensitySparklines
createEventPlotting	createEventPlotting
createGroup	createGroup
createGroupByAttribute	createGroupByAttribute
createGroupById	createGroupById
createGroupFromInput	createGroupFromInput
createJunctionsTemplate	createJunctionsTemplate
createOptimalSurvData	createOptimalSurvData
createSparklines	createSparklines
customColMedians	customRowMeans
customRowMaxs	customRowMeans
customRowMeans	customRowMeans
customRowMedians	customRowMeans
customRowMins	customRowMeans
customRowRanges	customRowMeans
customRowVars	customRowMeans
dataServer	appServer
dataUI	appUI
diagramSplicingEvent	diagramSplicingEvent
diffAnalyses	diffAnalyses
diffEventServer	appServer
diffEventUI	appUI
diffExpressionEventServer	appServer
diffExpressionEventUI	appUI
diffExpressionServer	appServer
diffExpressionSet	diffExpressionSet
diffExpressionTableServer	appServer
diffExpressionTableUI	appUI
diffExpressionUI	appUI
diffSplicingEventServer	appServer
diffSplicingEventUI	appUI
diffSplicingServer	appServer
diffSplicingSet	diffSplicingSet
diffSplicingTableServer	appServer
diffSplicingTableUI	appUI
diffSplicingUI	appUI
dimReductionServer	appServer
dimReductionUI	appUI
disableTab	disableTab
discardLowCoveragePSIvalues	discardLowCoveragePSIvalues
discardOutsideSamplesFromGroups	discardOutsideSamplesFromGroups
display	display
downloadFiles	downloadFiles
enableTab	disableTab
endProcess	startProcess
ensemblToUniprot	ensemblToUniprot
errorAlert	showAlert
errorDialog	inlineDialog
errorModal	styleModal
escape	escape
eventPlotOptions	eventPlotOptions
exportGroupsToFile	exportGroupsToFile
export_highcharts	export_highcharts
fileBrowser	fileBrowser
fileBrowserInfoInput	fileBrowserInput
fileBrowserInput	fileBrowserInput
filterGeneExpr	filterGeneExpr
filterGroups	filterGroups
filterPSI	filterPSI
findASeventsFromGene	findASeventsFromGene
findEventData	findEventData
firebrowseServer	appServer
firebrowseUI	appUI
fisher	wilcox
fligner	wilcox
geneExprFileInput	geneExprFileInput
geneExprSurvSet	geneExprSurvSet
geNormalisationFilteringInterface	geNormalisationFilteringInterface
geNormalisationFilteringServer	appServer
geNormalisationFilteringUI	appUI
getActiveDataset	getGlobal
getAnnotationName	getGlobal
getASevent	getGlobal
getASevents	getGlobal
getAssemblyVersion	getGlobal
getAttributesTime	getAttributesTime
getAutoNavigation	getGlobal
getCategories	getGlobal
getCategory	getGlobal
getCategoryData	getGlobal
getClinicalData	getGlobal
getClinicalDataForSurvival	getClinicalDataForSurvival
getClinicalMatchFrom	getClinicalMatchFrom
getCores	getGlobal
getCorrelation	getGlobal
getData	getData
getDataRows	getDataRows
getDifferentialExpression	getDifferentialExpression
getDifferentialExpressionColumns	getDifferentialExpression
getDifferentialExpressionFiltered	getDifferentialExpression
getDifferentialExpressionResetPaging	getDifferentialExpression
getDifferentialExpressionSurvival	getDifferentialExpression
getDifferentialSplicing	getDifferentialSplicing
getDifferentialSplicingColumns	getDifferentialSplicing
getDifferentialSplicingFiltered	getDifferentialSplicing
getDifferentialSplicingResetPaging	getDifferentialSplicing
getDifferentialSplicingSurvival	getDifferentialSplicing
getDownloadsFolder	getDownloadsFolder
getEvent	getGlobal
getFirebrowseCohorts	getTCGAdataTypes
getFirebrowseDataTypes	getTCGAdataTypes
getFirebrowseDateFormat	getFirebrowseDateFormat
getFirebrowseDates	getTCGAdataTypes
getGeneExpression	getGlobal
getGeneList	getGeneList
getGenes	getGlobal
getGenesFromSplicingEvents	getSplicingEventFromGenes
getGlobal	getGlobal
getGroupIndependenceTesting	getGlobal
getGroups	getGroups
getGtexDataTypes	getGtexDataTypes
getGtexDataURL	getGtexDataURL
getGtexReleases	getGtexDataTypes
getGtexTissues	getGtexTissues
getHidden	getHidden
getHighlightedPoints	getHighlightedPoints
getICA	getGlobal
getInclusionLevels	getGlobal
getInclusionLevelsSummaryStatsCache	getGlobal
getJunctionQuantification	getGlobal
getLabelledPoints	getHighlightedPoints
getMatchingSamples	getSampleFromSubject
getNumerics	getNumerics
getPatientFromSample	getSubjectFromSample
getPCA	getGlobal
getPrecision	getGlobal
getSampleAttributes	getGlobal
getSampleFromPatient	getSampleFromSubject
getSampleFromSubject	getSampleFromSubject
getSampleId	getGlobal
getSampleInfo	getGlobal
getSelectedDataPanel	getSelectedDataPanel
getSelectedGroups	selectGroupsUI
getSelectedPoints	getHighlightedPoints
getServerFunctions	getServerFunctions
getSignificant	getGlobal
getSpecies	getGlobal
getSplicingEventCoordinates	getSplicingEventCoordinates
getSplicingEventData	getSplicingEventData
getSplicingEventFromGenes	getSplicingEventFromGenes
getSplicingEventTypes	getSplicingEventTypes
getSubjectAttributes	getGlobal
getSubjectFromSample	getSubjectFromSample
getSubjectId	getGlobal
getTCGAcohorts	getTCGAdataTypes
getTCGAdataTypes	getTCGAdataTypes
getTCGAdates	getTCGAdataTypes
getUiFunctions	getUiFunctions
getURLtoDownload	getGlobal
getValidEvents	getValidEvents
getValuePerPatient	assignValuePerSubject
getValuePerSubject	assignValuePerSubject
getZoom	getHighlightedPoints
ggplotAuxServer	ggplotServer
ggplotServer	ggplotServer
ggplotTooltip	ggplotTooltip
ggplotUI	ggplotUI
globalSelectize	globalSelectize
groupByAttribute	groupByAttribute
groupByExpression	groupByAttribute
groupByGrep	groupByAttribute
groupById	groupByAttribute
groupByPreMadeList	groupByAttribute
groupManipulation	groupManipulation
groupManipulationInput	groupManipulationInput
groupPerElem	groupPerElem
groupsServer	appServer
groupsServerOnce	groupsServerOnce
groupsUI	appUI
gtexDataServer	appServer
gtexDataUI	appUI
hchart.survfit	hchart.survfit
hc_scatter	hc_scatter
helpServer	appServer
helpUI	appUI
HTMLfast	HTMLfast
icaServer	appServer
icaUI	appUI
importGroupsFrom	importGroupsFrom
inclusionLevelsFilterInterface	inclusionLevelsFilterInterface
inclusionLevelsFilterServer	appServer
inclusionLevelsFilterUI	appUI
inclusionLevelsInterface	inclusionLevelsInterface
inclusionLevelsServer	appServer
inclusionLevelsUI	appUI
infoModal	styleModal
infoServer	appServer
infoUI	appUI
inlineDialog	inlineDialog
insideFile	insideFile
is.whole	is.whole
isFile	isFile
isFirebrowseUp	isFirebrowseUp
isRStudioServer	isRStudioServer
joinEventsPerType	joinEventsPerType
junctionQuantFileInput	geneExprFileInput
junctionString	junctionString
kruskal	wilcox
labelBasedOnCutoff	labelBasedOnCutoff
levene	wilcox
leveneTest	leveneTest
linkToArticles	linkToArticles
linkToRunJS	linkToRunJS
listAllAnnotations	listAllAnnotations
listSplicingAnnotations	listSplicingAnnotations
loadAnnotation	loadAnnotation
loadBy	loadBy
loadCustomSplicingAnnotationSet	loadCustomSplicingAnnotationSet
loadedDataModal	loadedDataModal
loadFile	loadFile
loadFileFormats	loadFileFormats
loadFirebrowseData	loadTCGAdata
loadFirebrowseFolders	loadFirebrowseFolders
loadGeneExpressionSet	loadGeneExpressionSet
loadGtexData	loadGtexData
loadGtexDataShiny	loadGtexDataShiny
loadGtexFile	loadGtexFile
loadLocalFiles	loadLocalFiles
loadRequiredData	missingDataModal
loadSplicingQuantificationSet	loadSplicingQuantificationSet
loadSRAproject	loadSRAproject
loadTCGAdata	loadTCGAdata
loadTCGAsampleMetadata	loadTCGAsampleMetadata
localDataServer	appServer
localDataUI	appUI
matchGroupASeventsAndGenes	matchGroupASeventsAndGenes
matchGroupSubjectsAndSamples	matchGroupSubjectsAndSamples
matchSplicingEventsWithGenes	matchSplicingEventsWithGenes
missingDataGuide	missingDataModal
missingDataModal	missingDataModal
modTabPanel	modTabPanel
navSelectize	navSelectize
normaliseGeneExpression	normaliseGeneExpression
normalizeGeneExpression	normaliseGeneExpression
operateOnGroups	operateOnGroups
optimalSurvivalCutoff	optimalSurvivalCutoff
optimSurvDiffSet	optimSurvDiffSet
parseCategoricalGroups	parseCategoricalGroups
parseDateResponse	parseDateResponse
parseFile	parseFile
parseFirebrowseMetadata	parseFirebrowseMetadata
parseMatsA3SS	parseMatsGeneric
parseMatsA5SS	parseMatsGeneric
parseMatsAFE	parseMatsGeneric
parseMatsALE	parseMatsGeneric
parseMatsAnnotation	parseMisoAnnotation
parseMatsEvent	parseMatsEvent
parseMatsGeneric	parseMatsGeneric
parseMatsMXE	parseMatsGeneric
parseMatsRI	parseMatsGeneric
parseMatsSE	parseMatsGeneric
parseMisoA3SS	parseMisoGeneric
parseMisoA5SS	parseMisoGeneric
parseMisoAFE	parseMisoGeneric
parseMisoALE	parseMisoGeneric
parseMisoAnnotation	parseMisoAnnotation
parseMisoEvent	parseMisoEvent
parseMisoEventID	parseMisoEventID
parseMisoGeneric	parseMisoGeneric
parseMisoId	parseMisoId
parseMisoMXE	parseMisoGeneric
parseMisoRI	parseMisoGeneric
parseMisoSE	parseMisoGeneric
parseMisoTandemUTR	parseMisoGeneric
parseSampleGroups	parseTcgaSampleInfo
parseSplicingEvent	parseSplicingEvent
parseSuppaA3SS	parseSuppaGeneric
parseSuppaA5SS	parseSuppaGeneric
parseSuppaAFE	parseSuppaGeneric
parseSuppaALE	parseSuppaGeneric
parseSuppaAnnotation	parseMisoAnnotation
parseSuppaEvent	parseSuppaEvent
parseSuppaGeneric	parseSuppaGeneric
parseSuppaMXE	parseSuppaGeneric
parseSuppaRI	parseSuppaGeneric
parseSuppaSE	parseSuppaGeneric
parseTCGAsampleInfo	parseTcgaSampleInfo
parseTcgaSampleInfo	parseTcgaSampleInfo
parseTCGAsampleTypes	parseTcgaSampleInfo
parseUniprotXML	parseUniprotXML
parseUrlsFromFirebrowseResponse	parseUrlsFromFirebrowseResponse
parseVastToolsA3SS	parseVastToolsSE
parseVastToolsA5SS	parseVastToolsSE
parseVastToolsAnnotation	parseMisoAnnotation
parseVastToolsEvent	parseVastToolsEvent
parseVastToolsRI	parseVastToolsSE
parseVastToolsSE	parseVastToolsSE
pcaServer	appServer
pcaUI	appUI
performICA	performICA
performPCA	performPCA
plot.GEandAScorrelation	plot.GEandAScorrelation
plotClusters	plotClusters
plotCorrelation	plot.GEandAScorrelation
plotDistribution	plotDistribution
plotGeneExprPerSample	plotGeneExprPerSample
plotGroupIndependence	plotGroupIndependence
plotICA	plotICA
plotLibrarySize	plotLibrarySize
plotPCA	plotPCA
plotPCAvariance	plotPCAvariance
plotPointsStyle	plotPointsStyle
plotProtein	plotProtein
plotRowStats	plotRowStats
plotSingleICA	plotSingleICA
plotSplicingEvent	plotSplicingEvent
plotSurvivalCurves	plotSurvivalCurves
plotSurvivalPvaluesByCutoff	plotSurvivalPvaluesByCutoff
plottableXranges	plottableXranges
plotTranscripts	plotTranscripts
plotVariance	plotPCAvariance
prepareAnnotationFromEvents	prepareAnnotationFromEvents
prepareEventPlotOptions	prepareEventPlotOptions
prepareFileBrowser	prepareFileBrowser
prepareFirebrowseArchives	prepareFirebrowseArchives
prepareGenePresentation	prepareGenePresentation
prepareGeneQuant	prepareSRAmetadata
prepareGeneQuantSTAR	prepareJunctionQuantSTAR
prepareJunctionQuant	prepareSRAmetadata
prepareJunctionQuantSTAR	prepareJunctionQuantSTAR
preparePreMadeGroupForSelection	preparePreMadeGroupForSelection
prepareSRAmetadata	prepareSRAmetadata
prepareWordBreak	prepareWordBreak
preserveAttributes	preserveAttributes
print.GEandAScorrelation	plot.GEandAScorrelation
processButton	processButton
processClickRedirection	analysesTableSet
processDatasetNames	processDatasetNames
processSRAdata	processSRAdata
processSurvData	processSurvData
processSurvival	processSurvival
processSurvTerms	processSurvTerms
psichomics	psichomics
pubmedUI	pubmedUI
quantifySplicing	quantifySplicing
quantifySplicingSet	quantifySplicingSet
queryEnsembl	queryEnsembl
queryEnsemblByEvent	queryEnsemblByGene
queryEnsemblByGene	queryEnsemblByGene
queryFirebrowseData	queryFirebrowseData
queryPubMed	queryPubMed
queryUniprot	queryUniprot
readAnnot	readAnnot
readFile	readFile
recountDataServer	appServer
recountDataUI	appUI
reduceDimensionality	reduceDimensionality
removeAlert	showAlert
renameDuplicated	renameDuplicated
renameGroups	renameGroups
renderBoxplot	renderBoxplot
renderDataTableSparklines	renderDataTableSparklines
renderGeneticInfo	renderGeneticInfo
renderGroupInterface	renderGroupInterface
renderProteinInfo	renderProteinInfo
replaceStrInList	replaceStrInList
rm.null	rm.null
roundDigits	roundDigits
roundMaxUp	roundMinDown
roundMinDown	roundMinDown
sampleInfoFileInput	geneExprFileInput
saveProcessedSRAdata	saveProcessedSRAdata
selectGroupsServer	selectGroupsUI
selectGroupsUI	selectGroupsUI
selectizeGeneInput	selectizeGeneInput
selectPreMadeGroup	selectPreMadeGroup
setActiveDataset	getGlobal
setAnnotationName	getGlobal
setASevent	getGlobal
setAssemblyVersion	getGlobal
setAutoNavigation	getGlobal
setCategory	getGlobal
setClinicalMatchFrom	getClinicalMatchFrom
setCores	getGlobal
setCorrelation	getGlobal
setData	getGlobal
setDataTable	getGlobal
setDifferentialExpression	getDifferentialExpression
setDifferentialExpressionColumns	getDifferentialExpression
setDifferentialExpressionFiltered	getDifferentialExpression
setDifferentialExpressionResetPaging	getDifferentialExpression
setDifferentialExpressionSurvival	getDifferentialExpression
setDifferentialSplicing	getDifferentialSplicing
setDifferentialSplicingColumns	getDifferentialSplicing
setDifferentialSplicingFiltered	getDifferentialSplicing
setDifferentialSplicingResetPaging	getDifferentialSplicing
setDifferentialSplicingSurvival	getDifferentialSplicing
setEvent	getGlobal
setFirebrowseData	setFirebrowseData
setGlobal	getGlobal
setGroupIndependenceTesting	getGlobal
setGroups	getGroups
setHidden	getHidden
setHighlightedPoints	getHighlightedPoints
setICA	getGlobal
setInclusionLevels	getGlobal
setInclusionLevelsSummaryStatsCache	getGlobal
setLabelledPoints	getHighlightedPoints
setLocalData	setLocalData
setMultipleFilesData	setLocalData
setNormalisedGeneExpression	getGlobal
setOperation	setOperation
setOperationIcon	setOperationIcon
setPCA	getGlobal
setPrecision	getGlobal
setSampleInfo	getGlobal
setSelectedDataPanel	getSelectedDataPanel
setSelectedPoints	getHighlightedPoints
setSignificant	getGlobal
setSpecies	getGlobal
setURLtoDownload	getGlobal
setZoom	getHighlightedPoints
showAlert	showAlert
showGroupsTable	showGroupsTable
sidebar	sidebar
signifDigits	signifDigits
singleDiffAnalyses	singleDiffAnalyses
sortCoordinates	sortCoordinates
spearman	wilcox
startProcess	startProcess
startProgress	startProgress
styleModal	styleModal
subjectInfoFileInput	geneExprFileInput
subjectMultiMatchWarning	subjectMultiMatchWarning
subsetGeneExpressionFromMatchingGenes	subsetGeneExpressionFromMatchingGenes
successAlert	showAlert
survdiffTerms	survdiffTerms
survfit.survTerms	survfit.survTerms
survivalServer	appServer
survivalUI	appUI
t.sticky	t.sticky
tabDataset	tabDataset
table2html	table2html
tableRow	tableRow
templateServer	appServer
templateUI	appUI
testGroupIndependence	testGroupIndependence
testSingleIndependence	testSingleIndependence
testSurvival	testSurvival
testSurvivalCutoff	testSurvivalCutoff
textSuggestions	textSuggestions
toJSarray	toJSarray
traceInList	traceInList
transformData	transformData
transformOptions	transformOptions
transformValues	transformValues
trimWhitespace	trimWhitespace
ttest	wilcox
uniqueBy	uniqueBy
updateClinicalParams	updateClinicalParams
updateFileBrowserInput	updateFileBrowserInput
updateProgress	startProgress
vennEvents	vennEvents
warningAlert	showAlert
warningDialog	inlineDialog
warningModal	styleModal
wilcox	wilcox
[.GEandAScorrelation	plot.GEandAScorrelation
[.sticky	t.sticky
