.addSeuratToMetaDataSCE	dot-addSeuratToMetaDataSCE
.checkDiffExpResultExists	dot-checkDiffExpResultExists
.computeSignificantPC	dot-computeSignificantPC
.extractSCEAnnotation	dot-extractSCEAnnotation
.formatDEAList	dot-formatDEAList
.getComponentNames	dot-getComponentNames
.ggBar	dot-ggBar
.ggDensity	dot-ggDensity
.ggScatter	dot-ggScatter
.ggViolin	dot-ggViolin
.sce2adata	dot-sce2adata
.seuratGetVariableFeatures	dot-seuratGetVariableFeatures
.seuratInvalidate	dot-seuratInvalidate
.updateAssaySCE	dot-updateAssaySCE
calcEffectSizes	calcEffectSizes
combineSCE	combineSCE
computeHeatmap	computeHeatmap
computeZScore	computeZScore
constructSCE	constructSCE
convertGeneIDs	convertGeneIDs
convertSCEToSeurat	convertSCEToSeurat
convertSeuratToSCE	convertSeuratToSCE
dataAnnotationColor	dataAnnotationColor
dedupRowNames	dedupRowNames
diffAbundanceFET	diffAbundanceFET
discreteColorPalette	discreteColorPalette
distinctColors	distinctColors
downSampleCells	downSampleCells
downSampleDepth	downSampleDepth
enrichRSCE	enrichRSCE
expData	expData
expData,ANY,character-method	expData-ANY-character-method
expData<-	expData-set
expData<-,ANY,character,CharacterOrNullOrMissing,logical-method	expData-set-ANY-character-CharacterOrNullOrMissing-logical-method
expDataNames	expDataNames
expDataNames,ANY-method	expDataNames-ANY-method
expDeleteDataTag	expDeleteDataTag
exportSCE	exportSCE
exportSCEtoAnnData	exportSCEtoAnnData
exportSCEtoFlatFile	exportSCEtoFlatFile
exportSCEToSeurat	exportSCEToSeurat
expSetDataTag	expSetDataTag
expTaggedData	expTaggedData
featureIndex	featureIndex
findMarkerDiffExp	findMarkerDiffExp
generateMeta	generateMeta
generateSimulatedData	generateSimulatedData
getBiomarker	getBiomarker
getMSigDBTable	getMSigDBTable
getSceParams	getSceParams
getTopHVG	getTopHVG
getTSNE	getTSNE
getUMAP	getUMAP
gsvaPlot	gsvaSCE
gsvaSCE	gsvaSCE
importAlevin	importAlevin
importAnnData	importAnnData
importBUStools	importBUStools
importCellRanger	importCellRanger
importCellRangerV2	importCellRanger
importCellRangerV2Sample	importCellRangerV2Sample
importCellRangerV3	importCellRanger
importCellRangerV3Sample	importCellRangerV3Sample
importDropEst	importDropEst
importExampleData	importExampleData
importFromFiles	importFromFiles
importGeneSetsFromCollection	importGeneSetsFromCollection
importGeneSetsFromGMT	importGeneSetsFromGMT
importGeneSetsFromList	importGeneSetsFromList
importGeneSetsFromMSigDB	importGeneSetsFromMSigDB
importMitoGeneSet	importMitoGeneSet
importMultipleSources	importMultipleSources
importOptimus	importOptimus
importSEQC	importSEQC
importSTARsolo	importSTARsolo
iterateSimulations	iterateSimulations
mergeSCEColData	mergeSCEColData
MitoGenes	MitoGenes
mouseBrainSubsetSCE	mouseBrainSubsetSCE
msigdb_table	msigdb_table
plotBarcodeRankDropsResults	plotBarcodeRankDropsResults
plotBarcodeRankScatter	plotBarcodeRankScatter
plotBatchVariance	plotBatchVariance
plotBcdsResults	plotBcdsResults
plotBiomarker	plotBiomarker
plotClusterAbundance	plotClusterAbundance
plotCxdsResults	plotCxdsResults
plotDecontXResults	plotDecontXResults
plotDEGHeatmap	plotDEGHeatmap
plotDEGRegression	plotDEGRegression
plotDEGViolin	plotDEGViolin
plotDimRed	plotDimRed
plotDoubletFinderResults	plotDoubletFinderResults
plotEmptyDropsResults	plotEmptyDropsResults
plotEmptyDropsScatter	plotEmptyDropsScatter
plotHeatmapMulti	plotHeatmapMulti
plotMarkerDiffExp	plotMarkerDiffExp
plotMASTThresholdGenes	plotMASTThresholdGenes
plotPCA	plotPCA
plotRunPerCellQCResults	plotRunPerCellQCResults
plotScDblFinderResults	plotScDblFinderResults
plotScdsHybridResults	plotScdsHybridResults
plotSCEBarAssayData	plotSCEBarAssayData
plotSCEBarColData	plotSCEBarColData
plotSCEBatchFeatureMean	plotSCEBatchFeatureMean
plotSCEDensity	plotSCEDensity
plotSCEDensityAssayData	plotSCEDensityAssayData
plotSCEDensityColData	plotSCEDensityColData
plotSCEDimReduceColData	plotSCEDimReduceColData
plotSCEDimReduceFeatures	plotSCEDimReduceFeatures
plotSCEHeatmap	plotSCEHeatmap
plotSCEScatter	plotSCEScatter
plotSCEViolin	plotSCEViolin
plotSCEViolinAssayData	plotSCEViolinAssayData
plotSCEViolinColData	plotSCEViolinColData
plotScrubletResults	plotScrubletResults
plotTopHVG	plotTopHVG
plotTSNE	plotTSNE
plotUMAP	plotUMAP
qcInputProcess	qcInputProcess
readSingleCellMatrix	readSingleCellMatrix
reportCellQC	reportCellQC
reportDiffExp	reportDiffExp
reportDropletQC	reportDropletQC
reportFindMarker	reportFindMarker
reportQCTool	reportQCTool
retrieveSCEIndex	retrieveSCEIndex
runANOVA	runANOVA
runBarcodeRankDrops	runBarcodeRankDrops
runBBKNN	runBBKNN
runBcds	runBcds
runCellQC	runCellQC
runComBatSeq	runComBatSeq
runCxds	runCxds
runCxdsBcdsHybrid	runCxdsBcdsHybrid
runDEAnalysis	runDEAnalysis
runDecontX	runDecontX
runDESeq2	runDESeq2
runDimensionalityReduction	runDimensionalityReduction
runDoubletFinder	runDoubletFinder
runDropletQC	runDropletQC
runEmptyDrops	runEmptyDrops
runFastMNN	runFastMNN
runFeatureSelection	runFeatureSelection
runKMeans	runKMeans
runLimmaBC	runLimmaBC
runLimmaDE	runLimmaDE
runMAST	runMAST
runMNNCorrect	runMNNCorrect
runNormalization	runNormalization
runPerCellQC	runPerCellQC
runSCANORAMA	runSCANORAMA
runScDblFinder	runScDblFinder
runSCMerge	runSCMerge
runScranSNN	runScranSNN
runScrublet	runScrublet
runSingleR	runSingleR
runWilcox	runWilcox
runZINBWaVE	runZINBWaVE
sampleSummaryStats	sampleSummaryStats
scaterCPM	scaterCPM
scaterlogNormCounts	scaterlogNormCounts
scaterPCA	scaterPCA
sce	sce
sceBatches	sceBatches
scranModelGeneVar	scranModelGeneVar
sctkListGeneSetCollections	sctkListGeneSetCollections
sctkPythonInstallConda	sctkPythonInstallConda
sctkPythonInstallVirtualEnv	sctkPythonInstallVirtualEnv
SEG	SEG
selectSCTKConda	selectSCTKConda
selectSCTKVirtualEnvironment	selectSCTKVirtualEnvironment
setSCTKDisplayRow	setSCTKDisplayRow
seuratComputeHeatmap	seuratComputeHeatmap
seuratComputeJackStraw	seuratComputeJackStraw
seuratElbowPlot	seuratElbowPlot
seuratFindClusters	seuratFindClusters
seuratFindHVG	seuratFindHVG
seuratFindMarkers	seuratFindMarkers
seuratGenePlot	seuratGenePlot
seuratHeatmapPlot	seuratHeatmapPlot
seuratICA	seuratICA
seuratIntegration	seuratIntegration
seuratJackStrawPlot	seuratJackStrawPlot
seuratNormalizeData	seuratNormalizeData
seuratPCA	seuratPCA
seuratPlotHVG	seuratPlotHVG
seuratReductionPlot	seuratReductionPlot
seuratReport	seuratReport
seuratRunTSNE	seuratRunTSNE
seuratRunUMAP	seuratRunUMAP
seuratScaleData	seuratScaleData
seuratSCTransform	seuratSCTransform
seuratVariableFeatures	seuratVariableFeatures
simpleLog	simpleLog
singleCellTK	singleCellTK
subDiffEx	subDiffEx
subDiffExANOVA	subDiffEx
subDiffExttest	subDiffEx
subsetSCECols	subsetSCECols
subsetSCERows	subsetSCERows
summarizeSCE	summarizeSCE
trimCounts	trimCounts
visPlot	visPlot
