scater-package	scater-package
arrange	arrange
arrange,SingleCellExperiment-method	arrange
bootstraps	bootstraps
bootstraps,SingleCellExperiment-method	bootstraps
bootstraps<-	bootstraps
bootstraps<-,SingleCellExperiment,array-method	bootstraps
calcAverage	calculateAverage
calculateAverage	calculateAverage
calculateCPM	calculateCPM
calculateFPKM	calculateFPKM
calculateQCMetrics	calculateQCMetrics
calculateTPM	calculateTPM
centreSizeFactors	centreSizeFactors
exprs	accessors
exprs,SingleCellExperiment-method,	accessors
exprs<-,SingleCellExperiment,ANY-method	accessors
filter	filter
filter,SingleCellExperiment-method	filter
fpkm	accessors
fpkm<-	accessors
getBMFeatureAnnos	getBMFeatureAnnos
getExplanatoryPCs	getExplanatoryPCs
getVarianceExplained	getVarianceExplained
isOutlier	isOutlier
librarySizeFactors	librarySizeFactors
multiplot	multiplot
mutate	mutate
mutate,SingleCellExperiment-method	mutate
nexprs	nexprs
normalize	normalize
normalize,SingleCellExperiment-method	normalize
normalizeCounts	normalizeCounts
normalizeSCE	normalize
norm_exprs	accessors
norm_exprs<-	accessors
plotColData	plotColData
plotDiffusionMap	plot_reddim
plotExplanatoryPCs	plotExplanatoryPCs
plotExplanatoryVariables	plotExplanatoryVariables
plotExpression	plotExpression
plotExprsFreqVsMean	plotExprsFreqVsMean
plotExprsVsTxLength	plotExprsVsTxLength
plotHeatmap	plotHeatmap
plotHighestExprs	plotHighestExprs
plotMDS	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
readSparseCounts	readSparseCounts
Reduced dimension plots	plot_reddim
rename	rename
rename,SingleCellExperiment-method	rename
runDiffusionMap	runDiffusionMap
runMDS	runMDS
runPCA,SingleCellExperiment-method	runPCA
runTSNE	runTSNE
runUMAP	runUMAP
scater-plot-args	scater-plot-args
scater-vis-var	scater-vis-var
SCESet	SCESet
SCESet-class	SCESet
sc_example_cell_info	sc_example_cell_info
sc_example_counts	sc_example_counts
stand_exprs	accessors
stand_exprs<-	accessors
sumCountsAcrossCells	sumCountsAcrossCells
sumCountsAcrossFeatures	sumCountsAcrossFeatures
toSingleCellExperiment	toSingleCellExperiment
uniquifyFeatureNames	uniquifyFeatureNames
updateSCESet	toSingleCellExperiment
