.activateAppOptionRegistry	registerAppOptions
.addCustomLabelsCommands	addCustomLabelsCommands
.addFacets	plot-utils
.addLabelCentersCommands	addLabelCentersCommands
.addMultiSelectionPlotCommands	addMultiSelectionCommands
.addSpecificTour	specific-tours
.addTourStep	addTourStep
.allowableChoiceError	validate-utils
.allowableColorByDataChoices	visual-parameters-generics
.allowableColorByDataChoices,DotPlot-method	DotPlot-class
.allowableXAxisChoices	metadata-plot-generics
.allowableXAxisChoices,ColumnDataPlot-method	ColumnDataPlot-class
.allowableXAxisChoices,RowDataPlot-method	RowDataPlot-class
.allowableYAxisChoices	metadata-plot-generics
.allowableYAxisChoices,ColumnDataPlot-method	ColumnDataPlot-class
.allowableYAxisChoices,RowDataPlot-method	RowDataPlot-class
.buildAes	aes-utils
.buildLabs	labs-utils
.cacheCommonInfo	setup-generics
.cacheCommonInfo,ColumnDataTable-method	ColumnDataTable-class
.cacheCommonInfo,ColumnDotPlot-method	ColumnDotPlot-class
.cacheCommonInfo,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.cacheCommonInfo,DotPlot-method	DotPlot-class
.cacheCommonInfo,Panel-method	Panel-class
.cacheCommonInfo,ReducedDimensionPlot-method	ReducedDimensionPlot-class
.cacheCommonInfo,RowDataTable-method	RowDataTable-class
.cacheCommonInfo,RowDotPlot-method	RowDotPlot-class
.checkboxGroupInput.iSEE	interface-wrappers
.checkboxInput.iSEE	interface-wrappers
.clearSpecificTours	specific-tours
.colorByNoneDotPlotField	plot-generics
.colorByNoneDotPlotField,DotPlot-method	DotPlot-class
.colorByNoneDotPlotScale	plot-generics
.colorByNoneDotPlotScale,DotPlot-method	DotPlot-class
.conditionalOnCheckGroup	conditional-utils
.conditionalOnCheckSolo	conditional-utils
.conditionalOnRadio	conditional-utils
.createCustomDimnamesModalObservers	createCustomDimnamesModalObservers
.createObservers	observer-generics
.createObservers,ColumnDataPlot-method	ColumnDataPlot-class
.createObservers,ColumnDotPlot-method	ColumnDotPlot-class
.createObservers,ColumnTable-method	ColumnTable-class
.createObservers,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.createObservers,DotPlot-method	DotPlot-class
.createObservers,FeatureAssayPlot-method	FeatureAssayPlot-class
.createObservers,Panel-method	Panel-class
.createObservers,ReducedDimensionPlot-method	ReducedDimensionPlot-class
.createObservers,RowDataPlot-method	RowDataPlot-class
.createObservers,RowDotPlot-method	RowDotPlot-class
.createObservers,RowTable-method	RowTable-class
.createObservers,SampleAssayPlot-method	SampleAssayPlot-class
.createObservers,Table-method	Table-class
.createProtectedParameterObservers	createProtectedParameterObservers
.createUnprotectedParameterObservers	createProtectedParameterObservers
.deactivateAppOptionRegistry	registerAppOptions
.defineDataInterface	interface-generics
.defineDataInterface,ColumnDataPlot-method	ColumnDataPlot-class
.defineDataInterface,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.defineDataInterface,FeatureAssayPlot-method	FeatureAssayPlot-class
.defineDataInterface,Panel-method	Panel-class
.defineDataInterface,ReducedDimensionPlot-method	ReducedDimensionPlot-class
.defineDataInterface,RowDataPlot-method	RowDataPlot-class
.defineDataInterface,SampleAssayPlot-method	SampleAssayPlot-class
.defineDataInterface,Table-method	Table-class
.defineInterface	interface-generics
.defineInterface,ColumnDotPlot-method	ColumnDotPlot-class
.defineInterface,ColumnTable-method	ColumnTable-class
.defineInterface,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.defineInterface,DotPlot-method	DotPlot-class
.defineInterface,Panel-method	Panel-class
.defineInterface,RowDotPlot-method	RowDotPlot-class
.defineInterface,RowTable-method	RowTable-class
.defineOutput	output-generics
.defineOutput,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.defineOutput,DotPlot-method	DotPlot-class
.defineOutput,Table-method	Table-class
.definePanelTour	documentation-generics
.definePanelTour,ColumnDataPlot-method	ColumnDataPlot-class
.definePanelTour,ColumnDataTable-method	ColumnDataTable-class
.definePanelTour,ColumnDotPlot-method	ColumnDotPlot-class
.definePanelTour,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.definePanelTour,DotPlot-method	DotPlot-class
.definePanelTour,FeatureAssayPlot-method	FeatureAssayPlot-class
.definePanelTour,Panel-method	Panel-class
.definePanelTour,ReducedDimensionPlot-method	ReducedDimensionPlot-class
.definePanelTour,RowDataPlot-method	RowDataPlot-class
.definePanelTour,RowDataTable-method	RowDataTable-class
.definePanelTour,RowDotPlot-method	RowDotPlot-class
.definePanelTour,SampleAssayPlot-method	SampleAssayPlot-class
.definePanelTour,Table-method	Table-class
.defineVisualColorInterface	visual-parameters-generics
.defineVisualColorInterface,DotPlot-method	DotPlot-class
.defineVisualFacetInterface	visual-parameters-generics
.defineVisualFacetInterface,DotPlot-method	DotPlot-class
.defineVisualOtherInterface	visual-parameters-generics
.defineVisualOtherInterface,DotPlot-method	DotPlot-class
.defineVisualPointInterface	visual-parameters-generics
.defineVisualPointInterface,DotPlot-method	DotPlot-class
.defineVisualShapeInterface	visual-parameters-generics
.defineVisualShapeInterface,DotPlot-method	DotPlot-class
.defineVisualSizeInterface	visual-parameters-generics
.defineVisualSizeInterface,DotPlot-method	DotPlot-class
.defineVisualTextInterface	visual-parameters-generics
.defineVisualTextInterface,DotPlot-method	DotPlot-class
.emptyDefault	class-utils
.exportOutput	output-generics
.exportOutput,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.exportOutput,DotPlot-method	DotPlot-class
.exportOutput,Panel-method	Panel-class
.exportOutput,Table-method	Table-class
.extractAssaySubmatrix	extractAssaySubmatrix
.findAtomicFields	cache-utils
.fullName	getEncodedName
.fullName,ColumnDataPlot-method	ColumnDataPlot-class
.fullName,ColumnDataTable-method	ColumnDataTable-class
.fullName,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.fullName,FeatureAssayPlot-method	FeatureAssayPlot-class
.fullName,ReducedDimensionPlot-method	ReducedDimensionPlot-class
.fullName,RowDataPlot-method	RowDataPlot-class
.fullName,RowDataTable-method	RowDataTable-class
.fullName,SampleAssayPlot-method	SampleAssayPlot-class
.generateDotPlot	plot-generics
.generateDotPlot,DotPlot-method	DotPlot-class
.generateDotPlotData	plot-generics
.generateDotPlotData,ColumnDataPlot-method	ColumnDataPlot-class
.generateDotPlotData,FeatureAssayPlot-method	FeatureAssayPlot-class
.generateDotPlotData,ReducedDimensionPlot-method	ReducedDimensionPlot-class
.generateDotPlotData,RowDataPlot-method	RowDataPlot-class
.generateDotPlotData,SampleAssayPlot-method	SampleAssayPlot-class
.generateOutput	output-generics
.generateOutput,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.generateOutput,DotPlot-method	DotPlot-class
.generateOutput,Table-method	Table-class
.generateTable	table-generics
.generateTable,ColumnDataTable-method	ColumnDataTable-class
.generateTable,RowDataTable-method	RowDataTable-class
.getCachedCommonInfo	setCachedCommonInfo
.getDotPlotColorHelp	documentation-generics
.getDotPlotColorHelp,ColumnDotPlot-method	ColumnDotPlot-class
.getDotPlotColorHelp,RowDotPlot-method	RowDotPlot-class
.getEncodedName	getEncodedName
.getFullName	getEncodedName
.getPanelColor	getPanelColor
.getSpecificTours	specific-tours
.hideInterface	interface-generics
.hideInterface,ColumnDotPlot-method	ColumnDotPlot-class
.hideInterface,ColumnTable-method	ColumnTable-class
.hideInterface,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.hideInterface,DotPlot-method	DotPlot-class
.hideInterface,Panel-method	Panel-class
.hideInterface,RowDotPlot-method	RowDotPlot-class
.hideInterface,RowTable-method	RowTable-class
.hideInterface,Table-method	Table-class
.isAssayNumeric	cache-utils
.multipleChoiceError	validate-utils
.multiSelectionActive	multi-select-generics
.multiSelectionActive,DotPlot-method	DotPlot-class
.multiSelectionActive,Panel-method	Panel-class
.multiSelectionActive,Table-method	Table-class
.multiSelectionAvailable	multi-select-generics
.multiSelectionAvailable,Panel-method	Panel-class
.multiSelectionClear	multi-select-generics
.multiSelectionClear,DotPlot-method	DotPlot-class
.multiSelectionClear,Panel-method	Panel-class
.multiSelectionCommands	multi-select-generics
.multiSelectionCommands,DotPlot-method	DotPlot-class
.multiSelectionCommands,Table-method	Table-class
.multiSelectionDimension	multi-select-generics
.multiSelectionDimension,ColumnDotPlot-method	ColumnDotPlot-class
.multiSelectionDimension,ColumnTable-method	ColumnTable-class
.multiSelectionDimension,DotPlot-method	DotPlot-class
.multiSelectionDimension,Panel-method	Panel-class
.multiSelectionDimension,RowDotPlot-method	RowDotPlot-class
.multiSelectionDimension,RowTable-method	RowTable-class
.multiSelectionInvalidated	multi-select-generics
.multiSelectionInvalidated,ColumnDataPlot-method	ColumnDataPlot-class
.multiSelectionInvalidated,ColumnDotPlot-method	ColumnDotPlot-class
.multiSelectionInvalidated,FeatureAssayPlot-method	FeatureAssayPlot-class
.multiSelectionInvalidated,Panel-method	Panel-class
.multiSelectionInvalidated,RowDataPlot-method	RowDataPlot-class
.multiSelectionInvalidated,RowDotPlot-method	RowDotPlot-class
.multiSelectionInvalidated,SampleAssayPlot-method	SampleAssayPlot-class
.multiSelectionRestricted	multi-select-generics
.multiSelectionRestricted,ColumnDotPlot-method	ColumnDotPlot-class
.multiSelectionRestricted,Panel-method	Panel-class
.multiSelectionRestricted,RowDotPlot-method	RowDotPlot-class
.multiSelectionRestricted,Table-method	Table-class
.numericInput.iSEE	interface-wrappers
.panelColor	getPanelColor
.panelColor,ColumnDataPlot-method	ColumnDataPlot-class
.panelColor,ColumnDataTable-method	ColumnDataTable-class
.panelColor,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.panelColor,FeatureAssayPlot-method	FeatureAssayPlot-class
.panelColor,ReducedDimensionPlot-method	ReducedDimensionPlot-class
.panelColor,RowDataPlot-method	RowDataPlot-class
.panelColor,RowDataTable-method	RowDataTable-class
.panelColor,SampleAssayPlot-method	SampleAssayPlot-class
.prioritizeDotPlotData	plot-generics
.prioritizeDotPlotData,DotPlot-method	DotPlot-class
.processMultiSelections	processMultiSelections
.radioButtons.iSEE	interface-wrappers
.refineParameters	setup-generics
.refineParameters,ColumnDataPlot-method	ColumnDataPlot-class
.refineParameters,ColumnDataTable-method	ColumnDataTable-class
.refineParameters,ColumnDotPlot-method	ColumnDotPlot-class
.refineParameters,ColumnTable-method	ColumnTable-class
.refineParameters,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.refineParameters,DotPlot-method	DotPlot-class
.refineParameters,FeatureAssayPlot-method	FeatureAssayPlot-class
.refineParameters,Panel-method	Panel-class
.refineParameters,ReducedDimensionPlot-method	ReducedDimensionPlot-class
.refineParameters,RowDataPlot-method	RowDataPlot-class
.refineParameters,RowDataTable-method	RowDataTable-class
.refineParameters,RowDotPlot-method	RowDotPlot-class
.refineParameters,RowTable-method	RowTable-class
.refineParameters,SampleAssayPlot-method	SampleAssayPlot-class
.refineParameters,Table-method	Table-class
.renderOutput	output-generics
.renderOutput,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
.renderOutput,DotPlot-method	DotPlot-class
.renderOutput,Panel-method	Panel-class
.renderOutput,Table-method	Table-class
.replaceMissingWithFirst	replaceMissingWithFirst
.requestActiveSelectionUpdate	requestUpdate
.requestCleanUpdate	requestUpdate
.requestUpdate	requestUpdate
.retrieveOutput	retrieveOutput
.selectInput.iSEE	interface-wrappers
.selectizeInput.iSEE	interface-wrappers
.setCachedCommonInfo	setCachedCommonInfo
.showSelectionDetails	table-generics
.showSelectionDetails,ColumnTable-method	ColumnTable-class
.showSelectionDetails,RowTable-method	RowTable-class
.singleSelectionDimension	single-select-generics
.singleSelectionDimension,ColumnDotPlot-method	ColumnDotPlot-class
.singleSelectionDimension,ColumnTable-method	ColumnTable-class
.singleSelectionDimension,Panel-method	Panel-class
.singleSelectionDimension,RowDotPlot-method	RowDotPlot-class
.singleSelectionDimension,RowTable-method	RowTable-class
.singleSelectionSlots	single-select-generics
.singleSelectionSlots,DotPlot-method	DotPlot-class
.singleSelectionSlots,FeatureAssayPlot-method	FeatureAssayPlot-class
.singleSelectionSlots,Panel-method	Panel-class
.singleSelectionSlots,SampleAssayPlot-method	SampleAssayPlot-class
.singleSelectionValue	single-select-generics
.singleSelectionValue,DotPlot-method	DotPlot-class
.singleSelectionValue,Panel-method	Panel-class
.singleSelectionValue,Table-method	Table-class
.singleStringError	validate-utils
.sliderInput.iSEE	interface-wrappers
.textEval	manage_commands
.trackMultiSelection	track-utils
.trackRelinkedSelection	track-utils
.trackSingleSelection	track-utils
.trackUpdate	track-utils
.validLogicalError	validate-utils
.validNumberError	validate-utils
.validStringError	validate-utils
.whichGroupable	cache-utils
.whichNumeric	cache-utils
aes-utils	aes-utils
assay,ExperimentColorMap,character-method	ExperimentColorMap-class
assay,ExperimentColorMap,numeric-method	ExperimentColorMap-class
assayColorMap	ExperimentColorMap-class
assayColorMap,ExperimentColorMap,character-method	ExperimentColorMap-class
assayColorMap,ExperimentColorMap,missing-method	ExperimentColorMap-class
assayColorMap,ExperimentColorMap,numeric-method	ExperimentColorMap-class
assayColorMap<-	ExperimentColorMap-class
assayColorMap<-,ExperimentColorMap,character-method	ExperimentColorMap-class
assayColorMap<-,ExperimentColorMap,numeric-method	ExperimentColorMap-class
assayNames,ExperimentColorMap-method	ExperimentColorMap-class
assayNames<-,ExperimentColorMap,ANY-method	ExperimentColorMap-class
assays,ExperimentColorMap-method	ExperimentColorMap-class
assays<-,ExperimentColorMap,list-method	ExperimentColorMap-class
cache-utils	cache-utils
checkColormapCompatibility	checkColormapCompatibility
class-utils	class-utils
class:ExperimentColorMap	ExperimentColorMap-class
cleanDataset	cleanDataset
cleanDataset,SingleCellExperiment-method	cleanDataset
cleanDataset,SummarizedExperiment-method	cleanDataset
colData,ExperimentColorMap-method	ExperimentColorMap-class
colData<-,ExperimentColorMap,ANY-method	ExperimentColorMap-class
colDataColorMap	ExperimentColorMap-class
colDataColorMap,ExperimentColorMap,character-method	ExperimentColorMap-class
colDataColorMap,ExperimentColorMap,missing-method	ExperimentColorMap-class
colDataColorMap<-	ExperimentColorMap-class
colDataColorMap<-,ExperimentColorMap,character-method	ExperimentColorMap-class
collapseBox	collapseBox
ColumnDataPlot	ColumnDataPlot-class
ColumnDataPlot-class	ColumnDataPlot-class
ColumnDataTable	ColumnDataTable-class
ColumnDataTable-class	ColumnDataTable-class
ColumnDotPlot-class	ColumnDotPlot-class
columnSelectionColorMap	selectionColorMap
ColumnTable-class	ColumnTable-class
ComplexHeatmapPlot	ComplexHeatmapPlot-class
ComplexHeatmapPlot-class	ComplexHeatmapPlot-class
createCustomPanels	createCustomPanels
createCustomPlot	createCustomPanels
createCustomTable	createCustomPanels
createLandingPage	createLandingPage
defaultTour	defaultTour
documentation-generics	documentation-generics
DotPlot-class	DotPlot-class
ExperimentColorMap	ExperimentColorMap-class
ExperimentColorMap-class	ExperimentColorMap-class
FeatureAssayPlot	FeatureAssayPlot-class
FeatureAssayPlot-class	FeatureAssayPlot-class
filterDT	filterDTColumn
filterDTColumn	filterDTColumn
getAllAppOptions	registerAppOptions
getAppOption	registerAppOptions
getPanelDefault	panelDefaults
initialize,ColumnDataPlot-method	ColumnDataPlot-class
initialize,ColumnDataTable-method	ColumnDataTable-class
initialize,ColumnDotPlot-method	ColumnDotPlot-class
initialize,ColumnTable-method	ColumnTable-class
initialize,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
initialize,DotPlot-method	DotPlot-class
initialize,FeatureAssayPlot-method	FeatureAssayPlot-class
initialize,Panel-method	Panel-class
initialize,ReducedDimensionPlot-method	ReducedDimensionPlot-class
initialize,RowDataPlot-method	RowDataPlot-class
initialize,RowDataTable-method	RowDataTable-class
initialize,RowDotPlot-method	RowDotPlot-class
initialize,RowTable-method	RowTable-class
initialize,SampleAssayPlot-method	SampleAssayPlot-class
initialize,Table-method	Table-class
interface-generics	interface-generics
interface-wrappers	interface-wrappers
iSEE	iSEE
iSEE-pkg	iSEE-pkg
iSEEOptions	iSEEOptions
jitterSquarePoints	jitterPoints
jitterViolinPoints	jitterPoints
lassoPoints	lassoPoints
manage_commands	manage_commands
metadata-plot-generics	metadata-plot-generics
multi-select-generics	multi-select-generics
multiSelectionToFactor	multiSelectionToFactor
observer-generics	observer-generics
output-generics	output-generics
Panel-class	Panel-class
panelDefaults	panelDefaults
plot-generics	plot-generics
plot-utils	plot-utils
ReducedDimensionPlot	ReducedDimensionPlot-class
ReducedDimensionPlot-class	ReducedDimensionPlot-class
registerAppOptions	registerAppOptions
rowData,ExperimentColorMap-method	ExperimentColorMap-class
rowData<-,ExperimentColorMap,ANY-method	ExperimentColorMap-class
rowDataColorMap	ExperimentColorMap-class
rowDataColorMap,ExperimentColorMap,character-method	ExperimentColorMap-class
rowDataColorMap,ExperimentColorMap,missing-method	ExperimentColorMap-class
rowDataColorMap<-	ExperimentColorMap-class
rowDataColorMap<-,ExperimentColorMap,character-method	ExperimentColorMap-class
RowDataPlot	RowDataPlot-class
RowDataPlot-class	RowDataPlot-class
RowDataTable	RowDataTable-class
RowDataTable-class	RowDataTable-class
RowDotPlot-class	RowDotPlot-class
rowSelectionColorMap	selectionColorMap
RowTable-class	RowTable-class
SampleAssayPlot	SampleAssayPlot-class
SampleAssayPlot-class	SampleAssayPlot-class
setup-generics	setup-generics
show,ExperimentColorMap-method	ExperimentColorMap-class
show,Panel-method	Panel-class
single-select-generics	single-select-generics
specific-tours	specific-tours
subsetPointsByGrid	subsetPointsByGrid
synchronizeAssays	synchronizeAssays
Table-class	Table-class
table-generics	table-generics
track-utils	track-utils
updateObject,ColumnDotPlot-method	ColumnDotPlot-class
updateObject,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
updateObject,DotPlot-method	DotPlot-class
updateObject,Panel-method	Panel-class
updateObject,RowDotPlot-method	RowDotPlot-class
updateObject,Table-method	Table-class
validate-utils	validate-utils
visual-parameters-generics	visual-parameters-generics
[[,ColumnDotPlot,ANY,ANY-method	ColumnDotPlot-class
[[,ColumnDotPlot-method	ColumnDotPlot-class
[[,ComplexHeatmapPlot,ANY,ANY-method	ComplexHeatmapPlot-class
[[,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
[[,DotPlot,ANY,ANY-method	DotPlot-class
[[,DotPlot-method	DotPlot-class
[[,Panel,ANY,ANY-method	Panel-class
[[,Panel-method	Panel-class
[[,RowDotPlot,ANY,ANY-method	RowDotPlot-class
[[,RowDotPlot-method	RowDotPlot-class
[[<-,ColumnDotPlot,ANY,ANY-method	ColumnDotPlot-class
[[<-,ColumnDotPlot-method	ColumnDotPlot-class
[[<-,ComplexHeatmapPlot,ANY,ANY-method	ComplexHeatmapPlot-class
[[<-,ComplexHeatmapPlot-method	ComplexHeatmapPlot-class
[[<-,DotPlot,ANY,ANY-method	DotPlot-class
[[<-,DotPlot-method	DotPlot-class
[[<-,Panel,ANY,ANY-method	Panel-class
[[<-,Panel-method	Panel-class
[[<-,RowDotPlot,ANY,ANY-method	RowDotPlot-class
[[<-,RowDotPlot-method	RowDotPlot-class
