scater-package	scater-package
areSizeFactorsCentred	areSizeFactorsCentred
arrange	arrange
arrange,SCESet-method	arrange
arrange.SCESet	arrange
bootstraps	bootstraps
bootstraps,SCESet-method	bootstraps
bootstraps.SCESet	bootstraps
bootstraps<-	bootstraps
bootstraps<-,SCESet,array-method	bootstraps
calcAverage	calcAverage
calcIsExprs	calcIsExprs
calculateCPM	calculateCPM
calculateFPKM	calculateFPKM
calculateQCMetrics	calculateQCMetrics
calculateTPM	calculateTPM
cellDist	cellPairwiseDistances
cellDist,SCESet-method	cellPairwiseDistances
cellDist<-	cellPairwiseDistances
cellDist<-,SCESet,dist-method	cellPairwiseDistances
cellDist<-,SCESet,matrix-method	cellPairwiseDistances
cellDistSCESet	cellPairwiseDistances
cellNames	cellNames
cellNames<-	cellNames
cellNames<-,SCESet,vector-method	cellNames
cellPairwiseDistances	cellPairwiseDistances
cellPairwiseDistances,SCESet-method	cellPairwiseDistances
cellPairwiseDistances.SCESet	cellPairwiseDistances
cellPairwiseDistances<-	cellPairwiseDistances
cellPairwiseDistances<-,SCESet,dist-method	cellPairwiseDistances
cellPairwiseDistances<-,SCESet,matrix-method	cellPairwiseDistances
counts	counts
counts,SCESet-method	counts
counts.SCESet	counts
counts<-,SCESet,matrix-method	counts
cpm	cpm
cpm,SCESet-method	cpm
cpm<-	cpm
cpm<-,SCESet,matrix-method	cpm
cpmSCESet	cpm
fData	fData
fData,SCESet-method	fData
fData<-,SCESet,AnnotatedDataFrame-method	fData
fData<-,SCESet,data.frame-method	fData
featDist	featurePairwiseDistances
featDist,SCESet-method	featurePairwiseDistances
featDist<-	featurePairwiseDistances
featDist<-,SCESet,dist-method	featurePairwiseDistances
featDist<-,SCESet,matrix-method	featurePairwiseDistances
featDistSCESet	featurePairwiseDistances
featureControlInfo	featureControlInfo
featureControlInfo,SCESet-method	featureControlInfo
featureControlInfo.SCESet	featureControlInfo
featureControlInfo<-	featureControlInfo
featureControlInfo<-,SCESet,AnnotatedDataFrame-method	featureControlInfo
featurePairwiseDistances	featurePairwiseDistances
featurePairwiseDistances,SCESet-method	featurePairwiseDistances
featurePairwiseDistances<-	featurePairwiseDistances
featurePairwiseDistances<-,SCESet,dist-method	featurePairwiseDistances
featurePairwiseDistances<-,SCESet,matrix-method	featurePairwiseDistances
featurePairwiseDistancesSCESet	featurePairwiseDistances
filter	filter
filter,SCESet-method	filter
filter.SCESet	filter
findImportantPCs	findImportantPCs
fpkm	fpkm
fpkm,SCESet-method	fpkm
fpkm.SCESet	fpkm
fpkm<-	fpkm
fpkm<-,SCESet,matrix-method	fpkm
fromCellDataSet	fromCellDataSet
getBMFeatureAnnos	getBMFeatureAnnos
getExprs	getExprs
get_exprs	get_exprs
get_exprs,SCESet-method	get_exprs
get_exprs.SCESet	get_exprs
isOutlier	isOutlier
isSpike	isSpike
isSpike,SCESet-method	isSpike
is_exprs	is_exprs
is_exprs,SCESet-method	is_exprs
is_exprs.SCESet	is_exprs
is_exprs<-	is_exprs
is_exprs<-,SCESet,matrix-method	is_exprs
mergeSCESet	mergeSCESet
multiplot	multiplot
mutate	mutate
mutate,SCESet-method	mutate
mutate.SCESet	mutate
newSCESet	newSCESet
nexprs	nexprs
normalise	normalize
normalise,SCESet-method	normalize
normaliseExprs	normaliseExprs
normalize	normalize
normalize,SCESet-method	normalize
normalize.SCESet	normalize
normalizeExprs	normaliseExprs
normliseExprs	normaliseExprs
norm_counts	norm_counts
norm_counts,SCESet-method	norm_counts
norm_counts.SCESet	norm_counts
norm_counts<-	norm_counts
norm_counts<-,SCESet,matrix-method	norm_counts
norm_cpm	norm_cpm
norm_cpm,SCESet-method	norm_cpm
norm_cpm.SCESet	norm_cpm
norm_cpm<-	norm_cpm
norm_cpm<-,SCESet,matrix-method	norm_cpm
norm_exprs	norm_exprs
norm_exprs,SCESet-method	norm_exprs
norm_exprs.SCESet	norm_exprs
norm_exprs<-	norm_exprs
norm_exprs<-,SCESet,matrix-method	norm_exprs
norm_fpkm	norm_fpkm
norm_fpkm,SCESet-method	norm_fpkm
norm_fpkm.SCESet	norm_fpkm
norm_fpkm<-	norm_fpkm
norm_fpkm<-,SCESet,matrix-method	norm_fpkm
norm_tpm	norm_tpm
norm_tpm,SCESet-method	norm_tpm
norm_tpm.SCESet	norm_tpm
norm_tpm<-	norm_tpm
norm_tpm<-,SCESet,matrix-method	norm_tpm
pData	pData
pData,SCESet-method	pData
pData<-,SCESet,AnnotatedDataFrame-method	pData
pData<-,SCESet,data.frame-method	pData
plot	plot
plot,SCESet,ANY-method	plot
plot,SCESet-method	plot
plotDiffusionMap	plotDiffusionMap
plotDiffusionMap,SCESet-method	plotDiffusionMap
plotDiffusionMapSCESet	plotDiffusionMap
plotExplanatoryVariables	plotExplanatoryVariables
plotExpression	plotExpression
plotExpression,data.frame-method	plotExpression
plotExpression,SCESet-method	plotExpression
plotExpressionDefault	plotExpression
plotExpressionSCESet	plotExpression
plotExprsFreqVsMean	plotExprsFreqVsMean
plotExprsVsTxLength	plotExprsVsTxLength
plotFeatureData	plotFeatureData
plotHighestExprs	plotHighestExprs
plotMDS	plotMDS
plotMDS,SCESet-method	plotMDS
plotMDSSCESet	plotMDS
plotMetadata	plotMetadata
plotPCA	plotPCA
plotPCA,SCESet-method	plotPCA
plotPCASCESet	plotPCA
plotPhenoData	plotPhenoData
plotPlatePosition	plotPlatePosition
plotQC	plotQC
plotReducedDIm	plotReducedDim
plotReducedDim	plotReducedDim
plotReducedDim,data.frame-method	plotReducedDim
plotReducedDim,SCESet-method	plotReducedDim
plotReducedDim.default	plotReducedDim
plotReducedDim.SCESet	plotReducedDim
plotRLE	plotRLE
plotRLE,SCESet-method	plotRLE
plotSCESet	plot
plotTSNE	plotTSNE
plotTSNE,SCESet-method	plotTSNE
read10XResults	read10XResults
readKallistoResults	readKallistoResults
readKallistoResultsOneSample	readKallistoResultsOneSample
readSalmonResults	readSalmonResults
readSalmonResultsOneSample	readSalmonResultsOneSample
readTxResults	readTxResults
redDim	reducedDimension
redDim,SCESet-method	reducedDimension
redDim.SCESet	reducedDimension
redDim<-	reducedDimension
redDim<-,SCESet,matrix-method	reducedDimension
reducedDimension	reducedDimension
reducedDimension,SCESet-method	reducedDimension
reducedDimension.SCESet	reducedDimension
reducedDimension<-	reducedDimension
reducedDimension<-,SCESet,matrix-method	reducedDimension
rename	rename
rename,SCESet-method	rename
rename.SCESet	rename
runKallisto	runKallisto
runSalmon	runSalmon
scater_gui	scater_gui
SCESet	SCESet
SCESet-class	SCESet
SCESet-subset	SCESet-subset
sc_example_cell_info	sc_example_cell_info
sc_example_counts	sc_example_counts
setSpike	setSpike
setSpike<-	setSpike
setSpike<-,SCESet,character-method	setSpike
setSpike<-,SCESet,NULL-method	setSpike
set_exprs	set_exprs
set_exprs<-	set_exprs
set_exprs<-,SCESet,ANY,matrix-method	set_exprs
set_exprs<-,SCESet,ANY,NULL-method	set_exprs
sizeFactors	sizeFactors
sizeFactors,SCESet-method	sizeFactors
sizeFactors.SCESet	sizeFactors
sizeFactors<-	sizeFactors
sizeFactors<-,SCESet,NULL-method	sizeFactors
sizeFactors<-,SCESet,numeric-method	sizeFactors
spikes	spikes
spikes,SCESet-method	spikes
stand_exprs	stand_exprs
stand_exprs,SCESet-method	stand_exprs
stand_exprs.SCESet	stand_exprs
stand_exprs<-	stand_exprs
stand_exprs<-,SCESet,matrix-method	stand_exprs
summariseExprsAcrossFeatures	summariseExprsAcrossFeatures
toCellDataSet	toCellDataSet
tpm	tpm
tpm,SCESet-method	tpm
tpm.SCESet	tpm
tpm<-	tpm
tpm<-,SCESet,matrix-method	tpm
updateSCESet	updateSCESet
whichSpike	whichSpike
whichSpike,SCESet-method	whichSpike
writeSCESet	writeSCESet
[,SCESet,ANY,ANY,ANY-method	SCESet-subset
[,SCESet,ANY,ANY-method	SCESet-subset
[,SCESet,ANY-method	SCESet-subset
