addObjectAttrs	addObjectAttrs
addTCGAdata	addTCGAdata
analysesPlotSet	analysesPlotSet
analysesServer	appServer
analysesTableSet	analysesTableSet
analysesUI	appUI
appendNewGroups	appendNewGroups
appServer	appServer
appUI	appUI
areSplicingEvents	areSplicingEvents
articleUI	articleUI
ASquantFileInput	ASquantFileInput
assignColours	assignColours
assignValuePerPatient	getValuePerPatient
assignValuePerSubject	getValuePerPatient
basicStats	basicStats
blendColours	blendColours
browserHistory	browserHistory
bsModal2	bsModal2
calculateInclusionLevels	calculateInclusionLevels
calculateLoadingsContribution	calculateLoadingsContribution
checkFileFormat	checkFileFormat
checkFirebrowse	checkFirebrowse
checkIntegrity	checkIntegrity
checkSurvivalInput	checkSurvivalInput
closeProgress	closeProgress
clusterICAset	clusterICAset
clusterSet	clusterSet
colourInputMod	colourInputMod
correlateGEandAS	correlateGEandAS
correlationServer	appServer
correlationUI	appUI
createDataTab	createDataTab
createDensitySparklines	createDensitySparklines
createEventPlotting	createEventPlotting
createGroup	createGroup
createGroupByAttribute	createGroupByAttribute
createGroupByColumn	createGroupByAttribute
createGroupById	createGroupById
createGroupFromInput	createGroupFromInput
createJunctionsTemplate	createJunctionsTemplate
createOptimalSurvData	createOptimalSurvData
createSparklines	createSparklines
dataServer	appServer
dataUI	appUI
diffAnalyses	diffAnalyses
diffAnalysis	diffAnalyses
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
display	display
downloadFiles	downloadFiles
enableTab	disableTab
endProcess	endProcess
ensemblToUniprot	ensemblToUniprot
errorAlert	showAlert
errorDialog	inlineDialog
errorModal	styleModal
escape	escape
eventPlotOptions	eventPlotOptions
export_highcharts	export_highcharts
fileBrowser	fileBrowser
fileBrowserInput	fileBrowserInput
filterGroups	filterGroups
findASeventsFromGene	findASeventsFromGene
firebrowseServer	appServer
firebrowseUI	appUI
fisher	fisher
fligner	fligner
geneExprFileInput	geneExprFileInput
geneExprSurvSet	geneExprSurvSet
geNormalisationFilteringInterface	geNormalisationFilteringInterface
geNormalisationFilteringServer	appServer
geNormalisationFilteringUI	appUI
getActiveDataset	getEvent
getAnnotationName	getEvent
getASevent	getASevent
getASevents	getASevents
getAssemblyVersion	getEvent
getAttributesTime	getAttributesTime
getAutoNavigation	getGlobal
getCategories	getEvent
getCategory	getEvent
getCategoryData	getEvent
getClinicalData	getEvent
getClinicalDataForSurvival	getClinicalDataForSurvival
getClinicalMatchFrom	getClinicalMatchFrom
getColumnsTime	getAttributesTime
getCores	getGlobal
getCorrelation	getEvent
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	getEvent
getFirebrowseCohorts	getFirebrowseCohorts
getFirebrowseDataTypes	getFirebrowseDataTypes
getFirebrowseDateFormat	getFirebrowseDateFormat
getFirebrowseDates	getFirebrowseDates
getFirehoseCohorts	getFirebrowseCohorts
getFirehoseDataTypes	getFirebrowseDataTypes
getFirehoseDates	getFirebrowseDates
getGeneExpression	getEvent
getGenes	getGenes
getGenesFromSplicingEvents	getGenesFromSplicingEvents
getGlobal	getGlobal
getGroupIndependenceTesting	getEvent
getGroups	getGroups
getGTExTissues	getGtexTissues
getGtexTissues	getGtexTissues
getHidden	getHidden
getHighlightedPoints	getHighlightedPoints
getICA	getEvent
getInclusionLevels	getEvent
getJunctionQuantification	getEvent
getLabelledPoints	getHighlightedPoints
getMatchingSamples	getMatchingSamples
getNumerics	getNumerics
getPatientAttributes	getEvent
getPatientFromSample	getPatientFromSample
getPatientId	getEvent
getPCA	getEvent
getPrecision	getGlobal
getPSIperPatient	getValuePerPatient
getSampleAttributes	getEvent
getSampleFromPatient	getMatchingSamples
getSampleFromSubject	getMatchingSamples
getSampleId	getEvent
getSampleInfo	getEvent
getSelectedGroups	selectGroupsUI
getSelectedPoints	getHighlightedPoints
getServerFunctions	getServerFunctions
getSignificant	getGlobal
getSpecies	getEvent
getSplicingEventCoordinates	getSplicingEventCoordinates
getSplicingEventFromGenes	getSplicingEventFromGenes
getSplicingEventTypes	getSplicingEventTypes
getSubjectFromSample	getPatientFromSample
getTCGAcohorts	getFirebrowseCohorts
getTCGAdates	getFirebrowseDates
getUiFunctions	getUiFunctions
getURLtoDownload	getEvent
getValidEvents	getValidEvents
getValuePerPatient	getValuePerPatient
getValuePerSubject	getValuePerPatient
getZoom	getHighlightedPoints
ggplotAuxServer	ggplotServer
ggplotServer	ggplotServer
ggplotTooltip	ggplotTooltip
ggplotUI	ggplotUI
globalSelectize	globalSelectize
groupByAttribute	groupByAttribute
groupByExpression	groupByExpression
groupByGrep	groupByGrep
groupById	groupById
groupManipulation	groupManipulation
groupManipulationInput	groupManipulationInput
groupPerElem	groupPerElem
groupPerPatient	groupPerElem
groupPerSample	groupPerElem
groupsServer	appServer
groupsServerOnce	groupsServerOnce
groupsUI	appUI
gtexDataServer	appServer
gtexDataUI	appUI
hchart.survfit	hchart.survfit
hc_scatter	hc_scatter
helpServer	appServer
helpUI	appUI
icaServer	appServer
icaUI	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
isFirehoseUp	isFirebrowseUp
isRStudioServer	isRStudioServer
joinEventsPerType	joinEventsPerType
junctionString	junctionString
kruskal	kruskal
labelBasedOnCutoff	labelBasedOnCutoff
levene	levene
leveneTest	leveneTest
linkToArticle	linkToArticle
linkToRunJS	linkToRunJS
listAllAnnotations	listAllAnnotations
listSplicingAnnotations	listSplicingAnnotations
loadAnnotation	loadAnnotation
loadBy	loadBy
loadCustomSplicingAnnotationSet	loadCustomSplicingAnnotationSet
loadedDataModal	loadedDataModal
loadFile	loadFile
loadFileFormats	loadFileFormats
loadFirebrowseData	loadFirebrowseData
loadFirebrowseFolders	loadFirebrowseFolders
loadFirehoseData	loadFirebrowseData
loadFirehoseFolders	loadFirebrowseFolders
loadGeneExpressionSet	loadGeneExpressionSet
loadGtexData	loadGtexData
loadGtexDataShiny	loadGtexDataShiny
loadGTExFile	loadGtexFile
loadGtexFile	loadGtexFile
loadLocalFiles	loadLocalFiles
loadRequiredData	missingDataModal
loadSplicingQuantificationSet	loadSplicingQuantificationSet
loadSRAproject	loadSRAproject
loadTCGAdata	loadFirebrowseData
loadTCGAfolders	loadFirebrowseFolders
loadTCGAsampleMetadata	loadTCGAsampleMetadata
localDataServer	appServer
localDataUI	appUI
matchGroupPatientsAndSamples	matchGroupPatientsAndSamples
matchSplicingEventsWithGenes	matchSplicingEventsWithGenes
missingDataGuide	missingDataModal
missingDataModal	missingDataModal
modTabPanel	modTabPanel
navSelectize	navSelectize
noinfo	noinfo
normaliseGeneExpression	normaliseGeneExpression
operateOnGroups	operateOnGroups
optimalPSIcutoff	optimalSurvivalCutoff
optimalSurvivalCutoff	optimalSurvivalCutoff
optimSurvDiffSet	optimSurvDiffSet
parseCategoricalGroups	parseCategoricalGroups
parseDateResponse	parseDateResponse
parseFirebrowseMetadata	parseFirebrowseMetadata
parseFirehoseMetadata	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	parseSampleGroups
parseSplicingEvent	parseSplicingEvent
parseSuppaA3SS	parseSuppaGeneric
parseSuppaA5SS	parseSuppaGeneric
parseSuppaAFE	parseSuppaGeneric
parseSuppaALE	parseSuppaGeneric
parseSuppaAnnotation	parseMisoAnnotation
parseSuppaEvent	parseSuppaEvent
parseSuppaGeneric	parseSuppaGeneric
parseSuppaMXE	parseSuppaGeneric
parseSuppaRI	parseSuppaGeneric
parseSuppaSE	parseSuppaGeneric
parseTCGAmetadata	parseFirebrowseMetadata
parseTCGAsampleInfo	parseTcgaSampleInfo
parseTcgaSampleInfo	parseTcgaSampleInfo
parseUniprotXML	parseUniprotXML
parseUrlsFromFirebrowseResponse	parseUrlsFromFirebrowseResponse
parseUrlsFromFirehoseResponse	parseUrlsFromFirebrowseResponse
parseValidFile	parseValidFile
parseVastToolsA3SS	parseVastToolsSE
parseVastToolsA5SS	parseVastToolsSE
parseVastToolsAnnotation	parseMisoAnnotation
parseVastToolsEvent	parseVastToolsEvent
parseVastToolsRI	parseVastToolsSE
parseVastToolsSE	parseVastToolsSE
patientMultiMatchWarning	patientMultiMatchWarning
pcaServer	appServer
pcaUI	appUI
performICA	performICA
performPCA	performPCA
plot.GEandAScorrelation	plotCorrelation
plotClusters	plotClusters
plotCorrelation	plotCorrelation
plotDensity	plotDistribution
plotDistribution	plotDistribution
plotGroupIndependence	plotGroupIndependence
plotICA	plotICA
plotPCA	plotPCA
plotPointsStyle	plotPointsStyle
plotProtein	plotProtein
plotSingleICA	plotSingleICA
plotSurvivalCurves	plotSurvivalCurves
plottableXranges	plottableXranges
plotTranscripts	plotTranscripts
plotVariance	plotVariance
prepareAnnotationFromEvents	prepareAnnotationFromEvents
prepareEventPlotOptions	prepareEventPlotOptions
prepareFileBrowser	prepareFileBrowser
prepareFirebrowseArchives	prepareFirebrowseArchives
prepareFirehoseArchives	prepareFirebrowseArchives
prepareGeneQuant	prepareSRAmetadata
prepareGeneQuantSTAR	prepareSRAmetadata
prepareJunctionQuant	prepareSRAmetadata
prepareJunctionQuantSTAR	prepareSRAmetadata
prepareSRAmetadata	prepareSRAmetadata
prepareTCGAarchives	prepareFirebrowseArchives
prepareWordBreak	prepareWordBreak
processButton	processButton
processDatasetNames	processDatasetNames
processSurvData	processSurvData
processSurvival	processSurvival
processSurvTerms	processSurvTerms
psichomics	psichomics
pubmedUI	pubmedUI
quantifySplicing	quantifySplicing
quantifySplicingSet	quantifySplicingSet
queryEnsembl	queryEnsembl
queryEnsemblByEvent	queryEnsemblByEvent
queryEnsemblByGene	queryEnsemblByGene
queryFirebrowseData	queryFirebrowseData
queryFirehoseData	queryFirebrowseData
queryPubMed	queryPubMed
queryUniprot	queryUniprot
readAnnot	readAnnot
readFile	readFile
recountDataServer	appServer
recountDataUI	appUI
reduceDimensionality	reduceDimensionality
removeAlert	showAlert
renameDuplicated	renameDuplicated
renameGroups	renameGroups
renderDataTableSparklines	renderDataTableSparklines
renderGeneticInfo	renderGeneticInfo
renderGroupInterface	renderGroupInterface
renderProteinInfo	renderProteinInfo
rm.null	rm.null
roundDigits	roundDigits
roundMaxUp	roundMinDown
roundMinDown	roundMinDown
rowMeans	rowMeans
rowVars	rowVars
selectGroupsServer	selectGroupsUI
selectGroupsUI	selectGroupsUI
selectizeGeneInput	selectizeGeneInput
setActiveDataset	getEvent
setAnnotationName	getEvent
setASevent	getEvent
setAssemblyVersion	getEvent
setAutoNavigation	getGlobal
setCategory	getEvent
setClinicalMatchFrom	getClinicalMatchFrom
setCores	getGlobal
setCorrelation	getEvent
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	getEvent
setFirebrowseData	setFirebrowseData
setGlobal	getGlobal
setGroupIndependenceTesting	getEvent
setGroups	getGroups
setHidden	getHidden
setHighlightedPoints	getHighlightedPoints
setICA	getEvent
setInclusionLevels	getEvent
setLabelledPoints	getHighlightedPoints
setLocalData	setLocalData
setMultipleFilesData	setLocalData
setNormalisedGeneExpression	getEvent
setOperation	setOperation
setOperationIcon	setOperationIcon
setPCA	getEvent
setPrecision	getGlobal
setSampleInfo	getEvent
setSelectedPoints	getHighlightedPoints
setSignificant	getGlobal
setSpecies	getEvent
setURLtoDownload	getEvent
setZoom	getHighlightedPoints
showAlert	showAlert
showGroupsTable	showGroupsTable
sidebar	sidebar
signifDigits	signifDigits
singleDiffAnalyses	singleDiffAnalyses
sortCoordinates	sortCoordinates
spearman	spearman
startProcess	startProcess
startProgress	startProgress
styleModal	styleModal
subsetGeneExpressionFromMatchingGenes	subsetGeneExpressionFromMatchingGenes
survdiff.survTerms	survdiff.survTerms
survfit.survTerms	survfit.survTerms
survivalServer	appServer
survivalUI	appUI
tabDataset	tabDataset
table2html	table2html
tableRow	tableRow
templateServer	appServer
templateUI	appUI
testGroupIndependence	testGroupIndependence
testSingleIndependence	testSingleIndependence
testSurvival	testSurvival
testSurvivalCutoff	testSurvivalCutoff
textSuggestions	textSuggestions
toJSarray	toJSarray
transformData	transformData
transformOptions	transformOptions
transformValues	transformValues
trimWhitespace	trimWhitespace
ttest	ttest
uniqueBy	uniqueBy
updateClinicalParams	updateClinicalParams
updateFileBrowserInput	updateFileBrowserInput
updateProgress	updateProgress
vennEvents	vennEvents
warningAlert	showAlert
warningDialog	inlineDialog
warningModal	styleModal
wilcox	wilcox
