.assignIndicesToWorkers	scater-utils
.bpNotSharedOrUp	scater-utils
.splitColsByWorkers	scater-utils
.splitRowsByWorkers	scater-utils
.splitVectorByWorkers	scater-utils
.subset2index	scater-utils
addPerCellQC	addPerCellQC
addPerFeatureQC	addPerCellQC
aggregateAcrossCells	sumCountsAcrossCells
aggregateAcrossCells,SingleCellExperiment-method	sumCountsAcrossCells
aggregateAcrossCells,SummarizedExperiment-method	sumCountsAcrossCells
aggregateAcrossFeatures	sumCountsAcrossFeatures
annotateBMFeatures	annotateBMFeatures
bootstraps	bootstraps
bootstraps,SingleCellExperiment-method	bootstraps
bootstraps<-	bootstraps
bootstraps<-,SingleCellExperiment,array-method	bootstraps
calculateAverage	calculateAverage
calculateAverage,ANY-method	calculateAverage
calculateAverage,SingleCellExperiment-method	calculateAverage
calculateAverage,SummarizedExperiment-method	calculateAverage
calculateCPM	calculateCPM
calculateCPM,ANY-method	calculateCPM
calculateCPM,SingleCellExperiment-method	calculateCPM
calculateCPM,SummarizedExperiment-method	calculateCPM
calculateDiffusionMap	runDiffusionMap
calculateDiffusionMap,ANY-method	runDiffusionMap
calculateDiffusionMap,SingleCellExperiment-method	runDiffusionMap
calculateDiffusionMap,SummarizedExperiment-method	runDiffusionMap
calculateFPKM	calculateFPKM
calculateMDS	runMDS
calculateMDS,ANY-method	runMDS
calculateMDS,SingleCellExperiment-method	runMDS
calculateMDS,SummarizedExperiment-method	runMDS
calculateNMF	runNMF
calculateNMF,ANY-method	runNMF
calculateNMF,SingleCellExperiment-method	runNMF
calculateNMF,SummarizedExperiment-method	runNMF
calculatePCA	runPCA
calculatePCA,ANY-method	runPCA
calculatePCA,SingleCellExperiment-method	runPCA
calculatePCA,SummarizedExperiment-method	runPCA
calculateQCMetrics	defunct
calculateTPM	calculateTPM
calculateTPM,ANY-method	calculateTPM
calculateTPM,SingleCellExperiment-method	calculateTPM
calculateTPM,SummarizedExperiment-method	calculateTPM
calculateTSNE	runTSNE
calculateTSNE,ANY-method	runTSNE
calculateTSNE,SingleCellExperiment-method	runTSNE
calculateTSNE,SummarizedExperiment-method	runTSNE
calculateUMAP	runUMAP
calculateUMAP,ANY-method	runUMAP
calculateUMAP,SingleCellExperiment-method	runUMAP
calculateUMAP,SummarizedExperiment-method	runUMAP
centreSizeFactors	defunct
computeLibraryFactors	librarySizeFactors
computeMedianFactors	medianSizeFactors
defunct	defunct
exprs	accessors
exprs,SingleCellExperiment-method,	accessors
exprs<-,SingleCellExperiment,ANY-method	accessors
fpkm	accessors
fpkm,SingleCellExperiment-method	accessors
fpkm<-	accessors
fpkm<-,SingleCellExperiment,ANY-method	accessors
getBMFeatureAnnos	annotateBMFeatures
getExplanatoryPCs	getExplanatoryPCs
getVarianceExplained	getVarianceExplained
getVarianceExplained,ANY-method	getVarianceExplained
getVarianceExplained,SummarizedExperiment-method	getVarianceExplained
ggcells	ggsce
ggfeatures	ggsce
isOutlier	isOutlier
librarySizeFactors	librarySizeFactors
librarySizeFactors,ANY-method	librarySizeFactors
librarySizeFactors,SummarizedExperiment-method	librarySizeFactors
logNormCounts	logNormCounts
logNormCounts,SingleCellExperiment-method	logNormCounts
logNormCounts,SummarizedExperiment-method	logNormCounts
makePerCellDF	makePerCellDF
makePerFeatureDF	makePerFeatureDF
medianSizeFactors	medianSizeFactors
medianSizeFactors,ANY-method	medianSizeFactors
medianSizeFactors,SummarizedExperiment-method	medianSizeFactors
mockSCE	mockSCE
multiplot	multiplot
nexprs	nexprs
nexprs,ANY-method	nexprs
nexprs,SummarizedExperiment-method	nexprs
normalize,SingleCellExperiment-method	defunct
normalizeCounts	normalizeCounts
normalizeCounts,ANY-method	normalizeCounts
normalizeCounts,SingleCellExperiment-method	normalizeCounts
normalizeCounts,SummarizedExperiment-method	normalizeCounts
norm_exprs	accessors
norm_exprs,SingleCellExperiment-method	accessors
norm_exprs<-	accessors
norm_exprs<-,SingleCellExperiment,ANY-method	accessors
numDetectedAcrossCells	numDetectedAcrossCells
numDetectedAcrossCells,ANY-method	numDetectedAcrossCells
numDetectedAcrossCells,SummarizedExperiment-method	numDetectedAcrossCells
numDetectedAcrossFeatures	numDetectedAcrossFeatures
numDetectedAcrossFeatures,ANY-method	numDetectedAcrossFeatures
numDetectedAcrossFeatures,SummarizedExperiment-method	numDetectedAcrossFeatures
perCellQCMetrics	perCellQCMetrics
perCellQCMetrics,ANY-method	perCellQCMetrics
perCellQCMetrics,SingleCellExperiment-method	perCellQCMetrics
perCellQCMetrics,SummarizedExperiment-method	perCellQCMetrics
perFeatureQCMetrics	perFeatureQCMetrics
perFeatureQCMetrics,ANY-method	perFeatureQCMetrics
perFeatureQCMetrics,SummarizedExperiment-method	perFeatureQCMetrics
plotColData	plotColData
plotDiffusionMap	plot_reddim
plotDots	plotDots
plotExplanatoryPCs	plotExplanatoryPCs
plotExplanatoryVariables	plotExplanatoryVariables
plotExpression	plotExpression
plotHeatmap	plotHeatmap
plotHighestExprs	plotHighestExprs
plotMDS	plot_reddim
plotNMF	plot_reddim
plotPCA	plot_reddim
plotPCA,SingleCellExperiment-method	plot_reddim
plotPCASCE	plot_reddim
plotPlatePosition	plotPlatePosition
plotReducedDim	plotReducedDim
plotRLE	plotRLE
plotRLE,SingleCellExperiment-method	plotRLE
plotRowData	plotRowData
plotScater	plotScater
plotTSNE	plot_reddim
plotUMAP	plot_reddim
quickPerCellQC	quickPerCellQC
readSparseCounts	readSparseCounts
Reduced dimension plots	plot_reddim
retrieveCellInfo	retrieveCellInfo
retrieveFeatureInfo	retrieveFeatureInfo
runColDataPCA	runColDataPCA
runDiffusionMap	runDiffusionMap
runMDS	runMDS
runMultiUMAP	runMultiUMAP
runNMF	runNMF
runPCA	runPCA
runPCA,SingleCellExperiment-method	runPCA
runTSNE	runTSNE
runUMAP	runUMAP
scater-plot-args	scater-plot-args
scater-utils	scater-utils
SCESet	SCESet
SCESet-class	SCESet
sc_example_cell_info	mockSCE
sc_example_counts	mockSCE
stand_exprs	accessors
stand_exprs,SingleCellExperiment-method,	accessors
stand_exprs<-	accessors
stand_exprs<-,SingleCellExperiment,ANY-method	accessors
sumCountsAcrossCells	sumCountsAcrossCells
sumCountsAcrossCells,ANY-method	sumCountsAcrossCells
sumCountsAcrossCells,SummarizedExperiment-method	sumCountsAcrossCells
sumCountsAcrossFeatures	sumCountsAcrossFeatures
sumCountsAcrossFeatures,ANY-method	sumCountsAcrossFeatures
sumCountsAcrossFeatures,SummarizedExperiment-method	sumCountsAcrossFeatures
toSingleCellExperiment	toSingleCellExperiment
uniquifyFeatureNames	uniquifyFeatureNames
updateSCESet	toSingleCellExperiment
