calcEffectSizes	calcEffectSizes
combineSCE	combineSCE
computeHeatmap	computeHeatmap
computeZScore	computeZScore
constructSCE	constructSCE
convertSCEToSeurat	convertSCEToSeurat
convertSeuratToSCE	convertSeuratToSCE
dedupRowNames	dedupRowNames
detectCellOutlier	detectCellOutlier
diffAbundanceFET	diffAbundanceFET
discreteColorPalette	discreteColorPalette
distinctColors	distinctColors
downSampleCells	downSampleCells
downSampleDepth	downSampleDepth
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	runFindMarker
findMarkerTopTable	getFindMarkerTopTable
generateHTANMeta	generateHTANMeta
generateMeta	generateMeta
generateSimulatedData	generateSimulatedData
getBiomarker	getBiomarker
getDEGTopTable	getDEGTopTable
getDiffAbundanceResults	getDiffAbundanceResults
getDiffAbundanceResults,SingleCellExperiment-method	getDiffAbundanceResults
getDiffAbundanceResults<-	getDiffAbundanceResults
getDiffAbundanceResults<-,SingleCellExperiment-method	getDiffAbundanceResults
getEnrichRResult	getEnrichRResult
getEnrichRResult,SingleCellExperiment-method	getEnrichRResult
getEnrichRResult<-	getEnrichRResult
getEnrichRResult<-,SingleCellExperiment-method	getEnrichRResult
getFindMarkerTopTable	getFindMarkerTopTable
getGenesetNamesFromCollection	getGenesetNamesFromCollection
getMSigDBTable	getMSigDBTable
getPathwayResultNames	getPathwayResultNames
getSampleSummaryStatsTable	getSampleSummaryStatsTable
getSampleSummaryStatsTable,SingleCellExperiment-method	getSampleSummaryStatsTable
getSceParams	getSceParams
getSeuratVariableFeatures	getSeuratVariableFeatures
getSoupX	getSoupX
getSoupX,SingleCellExperiment-method	getSoupX
getSoupX<-	getSoupX
getSoupX<-,SingleCellExperiment-method	getSoupX
getTopHVG	getTopHVG
getTSCANResults	getTSCANResults
getTSCANResults,SingleCellExperiment-method	getTSCANResults
getTSCANResults<-	getTSCANResults
getTSCANResults<-,SingleCellExperiment-method	getTSCANResults
getTSNE	runTSNE
getUMAP	runUMAP
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
listSampleSummaryStatsTables	listSampleSummaryStatsTables
listSampleSummaryStatsTables,SingleCellExperiment-method	listSampleSummaryStatsTables
listTSCANResults	getTSCANResults
listTSCANResults,SingleCellExperiment-method	getTSCANResults
listTSCANTerminalNodes	getTSCANResults
listTSCANTerminalNodes,SingleCellExperiment-method	getTSCANResults
mergeSCEColData	mergeSCEColData
MitoGenes	MitoGenes
mouseBrainSubsetSCE	mouseBrainSubsetSCE
msigdb_table	msigdb_table
plotBarcodeRankDropsResults	plotBarcodeRankDropsResults
plotBarcodeRankScatter	plotBarcodeRankScatter
plotBatchCorrCompare	plotBatchCorrCompare
plotBatchVariance	plotBatchVariance
plotBcdsResults	plotBcdsResults
plotBubble	plotBubble
plotClusterAbundance	plotClusterAbundance
plotCxdsResults	plotCxdsResults
plotDecontXResults	plotDecontXResults
plotDEGHeatmap	plotDEGHeatmap
plotDEGRegression	plotDEGRegression
plotDEGViolin	plotDEGViolin
plotDEGVolcano	plotDEGVolcano
plotDimRed	plotDimRed
plotDoubletFinderResults	plotDoubletFinderResults
plotEmptyDropsResults	plotEmptyDropsResults
plotEmptyDropsScatter	plotEmptyDropsScatter
plotFindMarkerHeatmap	plotFindMarkerHeatmap
plotMarkerDiffExp	plotFindMarkerHeatmap
plotMASTThresholdGenes	plotMASTThresholdGenes
plotPathway	plotPathway
plotPCA	plotPCA
plotRunPerCellQCResults	plotRunPerCellQCResults
plotScanpyDotPlot	plotScanpyDotPlot
plotScanpyEmbedding	plotScanpyEmbedding
plotScanpyHeatmap	plotScanpyHeatmap
plotScanpyHVG	plotScanpyHVG
plotScanpyMarkerGenes	plotScanpyMarkerGenes
plotScanpyMarkerGenesDotPlot	plotScanpyMarkerGenesDotPlot
plotScanpyMarkerGenesHeatmap	plotScanpyMarkerGenesHeatmap
plotScanpyMarkerGenesMatrixPlot	plotScanpyMarkerGenesMatrixPlot
plotScanpyMarkerGenesViolin	plotScanpyMarkerGenesViolin
plotScanpyMatrixPlot	plotScanpyMatrixPlot
plotScanpyPCA	plotScanpyPCA
plotScanpyPCAGeneRanking	plotScanpyPCAGeneRanking
plotScanpyPCAVariance	plotScanpyPCAVariance
plotScanpyViolin	plotScanpyViolin
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
plotSeuratElbow	plotSeuratElbow
plotSeuratGenes	plotSeuratGenes
plotSeuratHeatmap	plotSeuratHeatmap
plotSeuratHVG	plotSeuratHVG
plotSeuratJackStraw	plotSeuratJackStraw
plotSeuratReduction	plotSeuratReduction
plotSoupXResults	plotSoupXResults
plotTopHVG	plotTopHVG
plotTSCANClusterDEG	plotTSCANClusterDEG
plotTSCANClusterPseudo	plotTSCANClusterPseudo
plotTSCANDimReduceFeatures	plotTSCANDimReduceFeatures
plotTSCANPseudotimeGenes	plotTSCANPseudotimeGenes
plotTSCANPseudotimeHeatmap	plotTSCANPseudotimeHeatmap
plotTSCANResults	plotTSCANResults
plotTSNE	plotTSNE
plotUMAP	plotUMAP
qcInputProcess	qcInputProcess
readSingleCellMatrix	readSingleCellMatrix
reportCellQC	reportCellQC
reportClusterAbundance	reportClusterAbundance
reportDiffAbundanceFET	reportDiffAbundanceFET
reportDiffExp	reportDiffExp
reportDropletQC	reportDropletQC
reportFindMarker	reportFindMarker
reportQCTool	reportQCTool
reportSeurat	reportSeurat
reportSeuratClustering	reportSeuratClustering
reportSeuratDimRed	reportSeuratDimRed
reportSeuratFeatureSelection	reportSeuratFeatureSelection
reportSeuratMarkerSelection	reportSeuratMarkerSelection
reportSeuratNormalization	reportSeuratNormalization
reportSeuratResults	reportSeuratResults
reportSeuratRun	reportSeuratRun
reportSeuratScaling	reportSeuratScaling
retrieveSCEIndex	retrieveSCEIndex
runANOVA	runDEAnalysis
runBarcodeRankDrops	runBarcodeRankDrops
runBBKNN	runBBKNN
runBcds	runBcds
runCellQC	runCellQC
runClusterSummaryMetrics	runClusterSummaryMetrics
runComBatSeq	runComBatSeq
runCxds	runCxds
runCxdsBcdsHybrid	runCxdsBcdsHybrid
runDEAnalysis	runDEAnalysis
runDecontX	runDecontX
runDESeq2	runDEAnalysis
runDimReduce	runDimReduce
runDoubletFinder	runDoubletFinder
runDropletQC	runDropletQC
runEmptyDrops	runEmptyDrops
runEnrichR	runEnrichR
runFastMNN	runFastMNN
runFeatureSelection	runFeatureSelection
runFindMarker	runFindMarker
runGSVA	runGSVA
runHarmony	runHarmony
runKMeans	runKMeans
runLimmaBC	runLimmaBC
runLimmaDE	runDEAnalysis
runMAST	runDEAnalysis
runMNNCorrect	runMNNCorrect
runModelGeneVar	runModelGeneVar
runNormalization	runNormalization
runPerCellQC	runPerCellQC
runQuickTSNE	runTSNE
runQuickUMAP	runUMAP
runSCANORAMA	runSCANORAMA
runScanpyFindClusters	runScanpyFindClusters
runScanpyFindHVG	runScanpyFindHVG
runScanpyFindMarkers	runScanpyFindMarkers
runScanpyNormalizeData	runScanpyNormalizeData
runScanpyPCA	runScanpyPCA
runScanpyScaleData	runScanpyScaleData
runScanpyTSNE	runScanpyTSNE
runScanpyUMAP	runScanpyUMAP
runScDblFinder	runScDblFinder
runSCMerge	runSCMerge
runScranSNN	runScranSNN
runScrublet	runScrublet
runSeuratFindClusters	runSeuratFindClusters
runSeuratFindHVG	runSeuratFindHVG
runSeuratFindMarkers	runSeuratFindMarkers
runSeuratHeatmap	runSeuratHeatmap
runSeuratICA	runSeuratICA
runSeuratIntegration	runSeuratIntegration
runSeuratJackStraw	runSeuratJackStraw
runSeuratNormalizeData	runSeuratNormalizeData
runSeuratPCA	runSeuratPCA
runSeuratScaleData	runSeuratScaleData
runSeuratSCTransform	runSeuratSCTransform
runSeuratTSNE	runSeuratTSNE
runSeuratUMAP	runSeuratUMAP
runSingleR	runSingleR
runSoupX	runSoupX
runTSCAN	runTSCAN
runTSCANClusterDEAnalysis	runTSCANClusterDEAnalysis
runTSCANDEG	runTSCANDEG
runTSNE	runTSNE
runUMAP	runUMAP
runVAM	runVAM
runWilcox	runDEAnalysis
runZINBWaVE	runZINBWaVE
sampleSummaryStats	sampleSummaryStats
scaterCPM	scaterCPM
scaterlogNormCounts	scaterlogNormCounts
scaterPCA	scaterPCA
sce	sce
sceBatches	sceBatches
sctkListGeneSetCollections	sctkListGeneSetCollections
sctkPythonInstallConda	sctkPythonInstallConda
sctkPythonInstallVirtualEnv	sctkPythonInstallVirtualEnv
SEG	SEG
selectSCTKConda	selectSCTKConda
selectSCTKVirtualEnvironment	selectSCTKVirtualEnvironment
setRowNames	setRowNames
setSampleSummaryStatsTable<-	getSampleSummaryStatsTable
setSampleSummaryStatsTable<-,SingleCellExperiment-method	getSampleSummaryStatsTable
setSCTKDisplayRow	setSCTKDisplayRow
setTopHVG	getTopHVG
singleCellTK	singleCellTK
subDiffEx	subDiffEx
subDiffExANOVA	subDiffEx
subDiffExttest	subDiffEx
subsetSCECols	subsetSCECols
subsetSCERows	subsetSCERows
summarizeSCE	summarizeSCE
trimCounts	trimCounts
