addClusters	addClusters
addClusters,ClusterExperiment,ClusterExperiment-method	addClusters
addClusters,ClusterExperiment,matrix-method	addClusters
addClusters,ClusterExperiment,numeric-method	addClusters
bigPalette	plottingFunctions
cluster01	clusterD
clusterContrasts	clusterContrasts
clusterContrasts,ClusterExperiment-method	clusterContrasts
clusterContrasts,vector-method	clusterContrasts
clusterD	clusterD
ClusterExperiment	ClusterExperiment-class
clusterExperiment	ClusterExperiment-class
clusterExperiment,matrix,ANY-method	ClusterExperiment-class
clusterExperiment,SummarizedExperiment,character-method	ClusterExperiment-class
clusterExperiment,SummarizedExperiment,factor-method	ClusterExperiment-class
clusterExperiment,SummarizedExperiment,matrix-method	ClusterExperiment-class
clusterExperiment,SummarizedExperiment,numeric-method	ClusterExperiment-class
ClusterExperiment-class	ClusterExperiment-class
ClusterExperiment-methods	ClusterExperiment-methods
clusterInfo	ClusterExperiment-methods
clusterInfo,ClusterExperiment-method	ClusterExperiment-methods
clusterK	clusterD
clusterLabels	ClusterExperiment-methods
clusterLabels,ClusterExperiment-method	ClusterExperiment-methods
clusterLabels<-	ClusterExperiment-methods
clusterLabels<-,ClusterExperiment,character-method	ClusterExperiment-methods
clusterLegend	ClusterExperiment-methods
clusterLegend,ClusterExperiment-method	ClusterExperiment-methods
clusterLegend<-	ClusterExperiment-methods
clusterLegend<-,ClusterExperiment,list-method	ClusterExperiment-methods
clusterMany	clusterMany
clusterMany,ClusterExperiment-method	clusterMany
clusterMany,list-method	clusterMany
clusterMany,matrix-method	clusterMany
clusterMany,SummarizedExperiment-method	clusterMany
clusterMatrix	ClusterExperiment-methods
clusterMatrix,ClusterExperiment-method	ClusterExperiment-methods
clusterMatrixNamed	ClusterExperiment-methods
clusterMatrixNamed,ClusterExperiment-method	ClusterExperiment-methods
clusterSingle	clusterSingle
clusterSingle,ClusterExperiment,missing-method	clusterSingle
clusterSingle,ClusterExperiment-method	clusterSingle
clusterSingle,matrix,missing-method	clusterSingle
clusterSingle,matrix-method	clusterSingle
clusterSingle,matrixOrMissing,matrixOrMissing-method	clusterSingle
clusterSingle,SummarizedExperiment,missing-method	clusterSingle
clusterSingle-methods	clusterSingle
clusterTypes	ClusterExperiment-methods
clusterTypes,ClusterExperiment-method	ClusterExperiment-methods
clusterTypes<-	ClusterExperiment-methods
clusterTypes<-,ClusterExperiment,character-method	ClusterExperiment-methods
coClustering	ClusterExperiment-methods
coClustering,ClusterExperiment-method	ClusterExperiment-methods
coClustering<-	ClusterExperiment-methods
coClustering<-,ClusterExperiment,matrix-method	ClusterExperiment-methods
combineMany	combineMany
combineMany,ClusterExperiment,character-method	combineMany
combineMany,ClusterExperiment,missing-method	combineMany
combineMany,ClusterExperiment,numeric-method	combineMany
combineMany,matrix,missing-method	combineMany
convertClusterLegend	convertClusterLegend
convertClusterLegend,ClusterExperiment-method	convertClusterLegend
getBestFeatures	getBestFeatures
getBestFeatures,ClusterExperiment-method	getBestFeatures
getBestFeatures,matrix-method	getBestFeatures
makeBlankData	plottingFunctions
makeDendrogram	makeDendrogram
makeDendrogram,ClusterExperiment-method	makeDendrogram
makeDendrogram,matrix-method	makeDendrogram
mergeClusters	mergeClusters
mergeClusters,ClusterExperiment-method	mergeClusters
mergeClusters,matrix-method	mergeClusters
nClusters	ClusterExperiment-methods
nClusters,ClusterExperiment-method	ClusterExperiment-methods
nFeatures	nFeatures
nFeatures,ClusterExperiment-method	ClusterExperiment-methods
nSamples	nSamples
nSamples,ClusterExperiment-method	ClusterExperiment-methods
orderSamples	ClusterExperiment-methods
orderSamples,ClusterExperiment-method	ClusterExperiment-methods
orderSamples<-	ClusterExperiment-methods
orderSamples<-,ClusterExperiment,numeric-method	ClusterExperiment-methods
plotClusters	plotClusters
plotClusters,ClusterExperiment,character-method	plotClusters
plotClusters,ClusterExperiment,missing-method	plotClusters
plotClusters,ClusterExperiment,numeric-method	plotClusters
plotClusters,matrix,missing-method	plotClusters
plotCoClustering	plotHeatmap
plotCoClustering,ClusterExperiment-method	plotHeatmap
plotDendrogram	makeDendrogram
plotDendrogram,ClusterExperiment-method	makeDendrogram
plotHeatmap	plotHeatmap
plotHeatmap,ClusterExperiment-method	plotHeatmap
plotHeatmap,matrix-method	plotHeatmap
plotHeatmap,SummarizedExperiment-method	plotHeatmap
plottingFunctions	plottingFunctions
primaryCluster	ClusterExperiment-methods
primaryCluster,ClusterExperiment-method	ClusterExperiment-methods
primaryClusterIndex	ClusterExperiment-methods
primaryClusterIndex,ClusterExperiment-method	ClusterExperiment-methods
primaryClusterIndex<-	ClusterExperiment-methods
primaryClusterIndex<-,ClusterExperiment,numeric-method	ClusterExperiment-methods
primaryClusterNamed	ClusterExperiment-methods
primaryClusterNamed,ClusterExperiment-method	ClusterExperiment-methods
removeClusters	addClusters
removeClusters,ClusterExperiment,character-method	addClusters
removeClusters,ClusterExperiment,numeric-method	addClusters
removeUnclustered	addClusters
removeUnclustered,ClusterExperiment-method	addClusters
RSEC	RSEC
RSEC,ClusterExperiment-method	RSEC
RSEC,matrix-method	RSEC
RSEC,SummarizedExperiment-method	RSEC
RSEC-methods	RSEC
seqCluster	seqCluster
seqPal1	plottingFunctions
seqPal2	plottingFunctions
seqPal3	plottingFunctions
seqPal4	plottingFunctions
seqPal5	plottingFunctions
setBreaks	plottingFunctions
setToCurrent	workflowClusters
setToCurrent,ClusterExperiment-method	workflowClusters
setToFinal	workflowClusters
setToFinal,ClusterExperiment-method	workflowClusters
show,ClusterExperiment-method	ClusterExperiment-methods
showBigPalette	plottingFunctions
showHeatmapPalettes	plottingFunctions
simCount	simData
simData	simData
subsampleClustering	subsampleClustering
transform	transform
transform,ClusterExperiment-method	transform
transformation	ClusterExperiment-methods
transformation,ClusterExperiment-method	ClusterExperiment-methods
trueCluster	simData
workflowClusterDetails	workflowClusters
workflowClusterDetails,ClusterExperiment-method	workflowClusters
workflowClusters	workflowClusters
workflowClusters,ClusterExperiment-method	workflowClusters
workflowClusterTable	workflowClusters
workflowClusterTable,ClusterExperiment-method	workflowClusters
[,ClusterExperiment,ANY,ANY,ANY-method	ClusterExperiment-methods
[,ClusterExperiment,ANY,character,ANY-method	ClusterExperiment-methods
[,ClusterExperiment,ANY,logical,ANY-method	ClusterExperiment-methods
[,ClusterExperiment,ANY,numeric,ANY-method	ClusterExperiment-methods
