scater-package	scater-package
areSizeFactorsCentred	areSizeFactorsCentred
arrange	arrange
arrange,SingleCellExperiment-method	arrange
bootstraps	bootstraps
bootstraps,SingleCellExperiment-method	bootstraps
bootstraps<-	bootstraps
bootstraps<-,SingleCellExperiment,array-method	bootstraps
calcAverage	calcAverage
calcIsExprs	calcIsExprs
calculateCPM	calculateCPM
calculateFPKM	calculateFPKM
calculateQCMetrics	calculateQCMetrics
calculateTPM	calculateTPM
centreSizeFactors	centreSizeFactors
downsampleCounts	downsampleCounts
exprs	accessors
exprs,SingleCellExperiment-method,	accessors
exprs<-,SingleCellExperiment,ANY-method	accessors
filter	filter
filter,SingleCellExperiment-method	filter
findImportantPCs	findImportantPCs
fpkm	accessors
fpkm<-	accessors
getBMFeatureAnnos	getBMFeatureAnnos
isOutlier	isOutlier
kallisto-wrapper	kallisto-wrapper
librarySizeFactors	librarySizeFactors
multiplot	multiplot
mutate	mutate
mutate,SingleCellExperiment-method	mutate
nexprs	nexprs
normalise	normalize
normalise,SingleCellExperiment-method	normalize
normaliseExprs	normalizeExprs
normalize	normalize
normalize,SingleCellExperiment-method	normalize
normalizeExprs	normalizeExprs
normalizeSCE	normalize
normliseExprs	normalizeExprs
norm_exprs	accessors
norm_exprs<-	accessors
plotCellData	plotColData
plotColData	plotColData
plotDiffusionMap	plot_reddim
plotExplanatoryVariables	plotExplanatoryVariables
plotExpression	plotExpression
plotExprsFreqVsMean	plotExprsFreqVsMean
plotExprsVsTxLength	plotExprsVsTxLength
plotFeatureData	plotRowData
plotHeatmap	plotHeatmap
plotHighestExprs	plotHighestExprs
plotMDS	plot_reddim
plotPCA	plot_reddim
plotPCA,SingleCellExperiment-method	plot_reddim
plotPCASCE	plot_reddim
plotPhenoData	plotColData
plotPlatePosition	plotPlatePosition
plotQC	plotQC
plotReducedDim	plotReducedDim
plotRLE	plotRLE
plotRLE,SingleCellExperiment-method	plotRLE
plotRowData	plotRowData
plotScater	plotScater
plotTSNE	plot_reddim
read10XResults	read10xResults
read10xResults	read10xResults
readKallistoResults	kallisto-wrapper
readKallistoResultsOneSample	kallisto-wrapper
readSalmonResults	salmon-wrapper
readSalmonResultsOneSample	salmon-wrapper
readTxResults	readTxResults
Reduced dimension plots	plot_reddim
rename	rename
rename,SingleCellExperiment-method	rename
runDiffusionMap	runDiffusionMap
runKallisto	kallisto-wrapper
runMDS	runMDS
runPCA	runPCA
runSalmon	salmon-wrapper
runTSNE	runTSNE
salmon-wrapper	salmon-wrapper
scater-plot-args	scater-plot-args
scater-vis-var	scater-vis-var
scater_gui	scater_gui
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
summariseExprsAcrossFeatures	summariseExprsAcrossFeatures
toSingleCellExperiment	toSingleCellExperiment
uniquifyFeatureNames	uniquifyFeatureNames
updateSCESet	toSingleCellExperiment
