scater-package	scater-package
accessors	accessors
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
deprecated	deprecated
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
fromCellDataSet	deprecated
getBMFeatureAnnos	getBMFeatureAnnos
getExprs	deprecated
isOutlier	isOutlier
kallisto-wrapper	kallisto-wrapper
multiplot	multiplot
mutate	mutate
mutate,SingleCellExperiment-method	mutate
newSCESet	newSCESet
nexprs	nexprs
normalise	normalize
normalise,SingleCellExperiment-method	normalize
normaliseExprs	normaliseExprs
normalize	normalize
normalize,SingleCellExperiment-method	normalize
normalizeExprs	normaliseExprs
normalizeSCE	normalize
normliseExprs	normaliseExprs
norm_exprs	accessors
norm_exprs<-	accessors
plotCellData	plotPhenoData
plotColData	plotPhenoData
plotDiffusionMap	plotDiffusionMap
plotDiffusionMap,SingleCellExperiment-method	plotDiffusionMap
plotExplanatoryVariables	plotExplanatoryVariables
plotExpression	plotExpression
plotExpression,data.frame-method	plotExpression
plotExpression,SingleCellExperiment-method	plotExpression
plotExpressionDefault	plotExpression
plotExprsFreqVsMean	plotExprsFreqVsMean
plotExprsVsTxLength	plotExprsVsTxLength
plotFeatureData	plotFeatureData
plotHighestExprs	plotHighestExprs
plotMDS	plotMDS
plotMDS,SingleCellExperiment-method	plotMDS
plotMetadata	plotMetadata
plotPCA	plotPCA
plotPCA,SingleCellExperiment-method	plotPCA
plotPCASCE	plotPCA
plotPhenoData	plotPhenoData
plotPlatePosition	plotPlatePosition
plotQC	plotQC
plotReducedDim	plotReducedDim
plotReducedDim,data.frame-method	plotReducedDim
plotReducedDim,SingleCellExperiment-method	plotReducedDim
plotReducedDimDefault	plotReducedDim
plotRLE	plotRLE
plotRLE,SingleCellExperiment-method	plotRLE
plotRowData	plotFeatureData
plotScater	plotScater
plotTSNE	plotTSNE
plotTSNE,SingleCellExperiment-method	plotTSNE
read10XResults	read10XResults
read10xResults	read10XResults
readKallistoResults	kallisto-wrapper
readKallistoResultsOneSample	kallisto-wrapper
readSalmonResults	salmon-wrapper
readSalmonResultsOneSample	salmon-wrapper
readTxResults	readTxResults
rename	rename
rename,SingleCellExperiment-method	rename
runDiffusionMap	plotDiffusionMap
runKallisto	kallisto-wrapper
runPCA	plotPCA
runSalmon	salmon-wrapper
runTSNE	plotTSNE
salmon-wrapper	salmon-wrapper
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
toCellDataSet	deprecated
toSingleCellExperiment	toSingleCellExperiment
updateSCESet	toSingleCellExperiment
