# iSEE Universe

## Documentation for package ‘iSEEu’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D F G I L M R S U V misc

## -- A --

AggregatedDotPlot | The AggregatedDotPlot class
AggregatedDotPlot-class | The AggregatedDotPlot class

## -- C --

createGeneSetCommands | Create gene set commands

## -- D --

defunct | Defunct functions
DifferentialStatisticsTable | Dynamic marker table
DynamicMarkerTable | Dynamic marker table
DynamicMarkerTable-class | Dynamic marker table
DynamicReducedDimensionPlot | Dynamic reduced dimension plot
DynamicReducedDimensionPlot-class | Dynamic reduced dimension plot

## -- F --

FeatureSetTable | Feature set table
FeatureSetTable-class | Feature set table

## -- G --

GeneSetTable | Gene set table
GeneSetTable-class | Gene set table
getAveAbFields | Register DE-related fields
getAveAbPattern | Global DE prefixes
getAveAbPatterns | Register DE-related fields
getFeatureSetCollections | Register feature set collections
getFeatureSetCommands | Register feature set collections
getLogFCFields | Register DE-related fields
getLogFCPattern | Global DE prefixes
getLogFCPatterns | Register DE-related fields
getPValueFields | Register DE-related fields
getPValuePattern | Global DE prefixes
getPValuePatterns | Register DE-related fields
getTableExtraFields | Global extra table fields

## -- I --

initialize-method | The AggregatedDotPlot class
initialize-method | Dynamic marker table
initialize-method | Dynamic reduced dimension plot
initialize-method | Feature set table
initialize-method | Gene set table
initialize-method | The LogFCLogFCPlot class
initialize-method | The MAPlot class
initialize-method | The MarkdownBoard class
initialize-method | The VolcanoPlot class

## -- L --

LogFCLogFCPlot | The LogFCLogFCPlot class
LogFCLogFCPlot-class | The LogFCLogFCPlot class

## -- M --

MAPlot | The MAPlot class
MAPlot-class | The MAPlot class
MarkdownBoard | The MarkdownBoard class
MarkdownBoard-class | The MarkdownBoard class
modeEmpty | App pre-configured to launch with no visible panel
modeGating | App pre-configured to link multiple feature assay plots
modeReducedDim | App pre-configured to compare multiple reduced dimension plots

## -- R --

registerAveAbFields | Register DE-related fields
registerAveAbPatterns | Register DE-related fields
registerDEFields | Register DE-related fields
registerFeatureSetCollections | Register feature set collections
registerFeatureSetCommands | Register feature set collections
registerLogFCFields | Register DE-related fields
registerLogFCPatterns | Register DE-related fields
registerPValueFields | Register DE-related fields
registerPValuePatterns | Register DE-related fields

## -- S --

setAveAbPattern | Global DE prefixes
setFeatureSetCommands | Global feature set commands
setLogFCPattern | Global DE prefixes
setPValuePattern | Global DE prefixes
setTableExtraFields | Global extra table fields

## -- U --

utils-geneset | Gene set utilities

## -- V --

VolcanoPlot | The VolcanoPlot class
VolcanoPlot-class | The VolcanoPlot class

## -- misc --

.allowableXAxisChoices-method | The LogFCLogFCPlot class
.allowableXAxisChoices-method | The MAPlot class
.allowableXAxisChoices-method | The VolcanoPlot class
.allowableYAxisChoices-method | The LogFCLogFCPlot class
.allowableYAxisChoices-method | The MAPlot class
.allowableYAxisChoices-method | The VolcanoPlot class
.cacheCommonInfo-method | The AggregatedDotPlot class
.cacheCommonInfo-method | Dynamic marker table
.cacheCommonInfo-method | Dynamic reduced dimension plot
.cacheCommonInfo-method | Feature set table
.cacheCommonInfo-method | The LogFCLogFCPlot class
.cacheCommonInfo-method | The MAPlot class
.cacheCommonInfo-method | The VolcanoPlot class
.colorByNoneDotPlotField-method | The LogFCLogFCPlot class
.colorByNoneDotPlotField-method | The MAPlot class
.colorByNoneDotPlotField-method | The VolcanoPlot class
.colorByNoneDotPlotScale-method | The LogFCLogFCPlot class
.colorByNoneDotPlotScale-method | The MAPlot class
.colorByNoneDotPlotScale-method | The VolcanoPlot class
.createObservers-method | The AggregatedDotPlot class
.createObservers-method | Dynamic marker table
.createObservers-method | Dynamic reduced dimension plot
.createObservers-method | Feature set table
.createObservers-method | Gene set table
.createObservers-method | The LogFCLogFCPlot class
.createObservers-method | The MAPlot class
.createObservers-method | The MarkdownBoard class
.createObservers-method | The VolcanoPlot class
.defineDataInterface-method | The AggregatedDotPlot class
.defineDataInterface-method | Dynamic marker table
.defineDataInterface-method | Dynamic reduced dimension plot
.defineDataInterface-method | Feature set table
.defineDataInterface-method | Gene set table
.defineDataInterface-method | The LogFCLogFCPlot class
.defineDataInterface-method | The MAPlot class
.defineDataInterface-method | The MarkdownBoard class
.defineDataInterface-method | The VolcanoPlot class
.defineInterface-method | The AggregatedDotPlot class
.defineOutput-method | The AggregatedDotPlot class
.defineOutput-method | Feature set table
.defineOutput-method | Gene set table
.defineOutput-method | The MarkdownBoard class
.definePanelTour-method | The AggregatedDotPlot class
.definePanelTour-method | Dynamic marker table
.definePanelTour-method | Dynamic reduced dimension plot
.definePanelTour-method | Feature set table
.definePanelTour-method | The LogFCLogFCPlot class
.definePanelTour-method | The MAPlot class
.definePanelTour-method | The MarkdownBoard class
.definePanelTour-method | The VolcanoPlot class
.exportOutput-method | The AggregatedDotPlot class
.exportOutput-method | The MarkdownBoard class
.fullName-method | The AggregatedDotPlot class
.fullName-method | Dynamic marker table
.fullName-method | Dynamic reduced dimension plot
.fullName-method | Feature set table
.fullName-method | Gene set table
.fullName-method | The LogFCLogFCPlot class
.fullName-method | The MAPlot class
.fullName-method | The MarkdownBoard class
.fullName-method | The VolcanoPlot class
.generateDotPlot-method | The LogFCLogFCPlot class
.generateDotPlot-method | The MAPlot class
.generateDotPlot-method | The VolcanoPlot class
.generateDotPlotData-method | Dynamic reduced dimension plot
.generateDotPlotData-method | The LogFCLogFCPlot class
.generateDotPlotData-method | The MAPlot class
.generateDotPlotData-method | The VolcanoPlot class
.generateOutput-method | The AggregatedDotPlot class
.generateOutput-method | Feature set table
.generateOutput-method | Gene set table
.generateOutput-method | The MarkdownBoard class
.generateTable-method | Dynamic marker table
.getAcceptableAveAbFields | Defunct functions
.getAcceptableLogFCFields | Defunct functions
.getAcceptablePValueFields | Defunct functions
.getDotPlotColorHelp-method | The LogFCLogFCPlot class
.getDotPlotColorHelp-method | The MAPlot class
.getDotPlotColorHelp-method | The VolcanoPlot class
.getGeneSetCommands | Gene set utilities
.getIdentifierType | Gene set utilities
.getOrganism | Gene set utilities
.hideInterface-method | The AggregatedDotPlot class
.hideInterface-method | Dynamic marker table
.hideInterface-method | Feature set table
.hideInterface-method | Gene set table
.hideInterface-method | The LogFCLogFCPlot class
.hideInterface-method | The MAPlot class
.hideInterface-method | The MarkdownBoard class
.hideInterface-method | The VolcanoPlot class
.multiSelectionActive-method | Feature set table
.multiSelectionActive-method | Gene set table
.multiSelectionAvailable-method | Feature set table
.multiSelectionAvailable-method | Gene set table
.multiSelectionClear-method | Feature set table
.multiSelectionClear-method | Gene set table
.multiSelectionCommands-method | Feature set table
.multiSelectionCommands-method | Gene set table
.multiSelectionDimension-method | Feature set table
.multiSelectionDimension-method | Gene set table
.multiSelectionInvalidated-method | Dynamic marker table
.multiSelectionInvalidated-method | Dynamic reduced dimension plot
.panelColor-method | The AggregatedDotPlot class
.panelColor-method | Dynamic marker table
.panelColor-method | Dynamic reduced dimension plot
.panelColor-method | Feature set table
.panelColor-method | Gene set table
.panelColor-method | The LogFCLogFCPlot class
.panelColor-method | The MAPlot class
.panelColor-method | The MarkdownBoard class
.panelColor-method | The VolcanoPlot class
.prioritizeDotPlotData-method | The LogFCLogFCPlot class
.prioritizeDotPlotData-method | The MAPlot class
.prioritizeDotPlotData-method | The VolcanoPlot class
.refineParameters-method | The AggregatedDotPlot class
.refineParameters-method | Dynamic marker table
.refineParameters-method | Dynamic reduced dimension plot
.refineParameters-method | Feature set table
.refineParameters-method | The LogFCLogFCPlot class
.refineParameters-method | The MAPlot class
.refineParameters-method | The VolcanoPlot class
.renderOutput-method | The AggregatedDotPlot class
.renderOutput-method | Feature set table
.renderOutput-method | Gene set table
.renderOutput-method | The MarkdownBoard class
.setAcceptableAveAbFields | Defunct functions
.setAcceptableLogFCFields | Defunct functions
.setAcceptablePValueFields | Defunct functions
.setGeneSetCommands | Gene set utilities
.setIdentifierType | Gene set utilities
.setOrganism | Gene set utilities