addClusters	addClusters
addClusters,ClusterExperiment,ClusterExperiment-method	addClusters
addClusters,ClusterExperiment,matrix-method	addClusters
addClusters,ClusterExperiment,numeric-method	addClusters
algorithmType	ClusterFunction-methods
algorithmType,character-method	ClusterFunction-methods
algorithmType,ClusterFunction-method	ClusterFunction-methods
algorithmType,factor-method	ClusterFunction-methods
bigPalette	plottingFunctions
clusterContrasts	clusterContrasts
clusterContrasts,ClusterExperiment-method	clusterContrasts
clusterContrasts,vector-method	clusterContrasts
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
ClusterFunction	ClusterFunction-class
clusterFunction	ClusterFunction-class
clusterFunction,function-method	ClusterFunction-class
ClusterFunction-class	ClusterFunction-class
ClusterFunction-methods	ClusterFunction-methods
clusterInfo	ClusterExperiment-methods
clusterInfo,ClusterExperiment-method	ClusterExperiment-methods
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,data.frame-method	clusterMany
clusterMany,list-method	clusterMany
clusterMany,matrix-method	clusterMany
clusterMany,SummarizedExperiment-method	clusterMany
clusterMatrix	ClusterExperiment-methods
clusterMatrix,ClusterExperiment,character-method	ClusterExperiment-methods
clusterMatrix,ClusterExperiment,missing-method	ClusterExperiment-methods
clusterMatrix,ClusterExperiment,numeric-method	ClusterExperiment-methods
clusterMatrixNamed	ClusterExperiment-methods
clusterMatrixNamed,ClusterExperiment-method	ClusterExperiment-methods
clusterSingle	clusterSingle
clusterSingle,ClusterExperiment,missing-method	clusterSingle
clusterSingle,matrixOrNULL,matrixOrNULL-method	clusterSingle
clusterSingle,matrixOrNULL,missing-method	clusterSingle
clusterSingle,missing,matrixOrNULL-method	clusterSingle
clusterSingle,SummarizedExperiment,missing-method	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	plottingFunctions
convertClusterLegend,ClusterExperiment-method	plottingFunctions
dendroClusterIndex	ClusterExperiment-methods
dendroClusterIndex,ClusterExperiment-method	ClusterExperiment-methods
getBestFeatures	getBestFeatures
getBestFeatures,ClusterExperiment-method	getBestFeatures
getBestFeatures,matrix-method	getBestFeatures
getBuiltInFunction	builtInClusteringFunctions
getBuiltInFunction,character-method	builtInClusteringFunctions
getClusterManyParams	getClusterManyParams
getClusterManyParams,ClusterExperiment-method	getClusterManyParams
getMergeCorrespond	mergeClusters
getMergeCorrespond,ClusterExperiment-method	mergeClusters
getPostProcessingArgs	mainClustering
getPostProcessingArgs,ClusterFunction-method	mainClustering
inputType	ClusterFunction-methods
inputType,character-method	ClusterFunction-methods
inputType,ClusterFunction-method	ClusterFunction-methods
inputType,factor-method	ClusterFunction-methods
internalFunctionCheck	ClusterFunction-class
listBuiltInFunctions	builtInClusteringFunctions
listBuiltInType01	builtInClusteringFunctions
listBuiltInTypeK	builtInClusteringFunctions
mainClustering	mainClustering
mainClustering,character-method	mainClustering
mainClustering,ClusterFunction-method	mainClustering
makeBlankData	plottingFunctions
makeDendrogram	makeDendrogram
makeDendrogram,ClusterExperiment-method	makeDendrogram
makeDendrogram,matrix-method	makeDendrogram
mergeClusterIndex	mergeClusters
mergeClusterIndex,ClusterExperiment-method	mergeClusters
mergeClusters	mergeClusters
mergeClusters,ClusterExperiment-method	mergeClusters
mergeClusters,matrix-method	mergeClusters
mergeCutoff	mergeClusters
mergeCutoff,ClusterExperiment-method	mergeClusters
mergeMethod	mergeClusters
mergeMethod,ClusterExperiment-method	mergeClusters
nClusters	ClusterExperiment-methods
nClusters,ClusterExperiment-method	ClusterExperiment-methods
nFeatures	ClusterExperiment-methods
nFeatures,ClusterExperiment-method	ClusterExperiment-methods
nodeMergeInfo	mergeClusters
nodeMergeInfo,ClusterExperiment-method	mergeClusters
nSamples	ClusterExperiment-methods
nSamples,ClusterExperiment-method	ClusterExperiment-methods
orderSamples	ClusterExperiment-methods
orderSamples,ClusterExperiment-method	ClusterExperiment-methods
orderSamples<-	ClusterExperiment-methods
orderSamples<-,ClusterExperiment,numeric-method	ClusterExperiment-methods
plotBarplot	plotBarplot
plotBarplot,ClusterExperiment,character-method	plotBarplot
plotBarplot,ClusterExperiment,missing-method	plotBarplot
plotBarplot,ClusterExperiment,numeric-method	plotBarplot
plotBarplot,matrix,missing-method	plotBarplot
plotBarplot,vector,missing-method	plotBarplot
plotClusters	plotClusters
plotClusters,ClusterExperiment,character-method	plotClusters
plotClusters,ClusterExperiment,missing-method	plotClusters
plotClusters,ClusterExperiment,numeric-method	plotClusters
plotClusters,matrix,missing-method	plotClusters
plotClustersWorkflow	plotClustersWorkflow
plotClustersWorkflow,ClusterExperiment-method	plotClustersWorkflow
plotCoClustering	plotHeatmap
plotCoClustering,ClusterExperiment-method	plotHeatmap
plotContrastHeatmap	plotContrastHeatmap
plotContrastHeatmap,ClusterExperiment-method	plotContrastHeatmap
plotDendrogram	plotDendrogram
plotDendrogram,ClusterExperiment-method	plotDendrogram
plotDimReduce	plotDimReduce
plotDimReduce,ClusterExperiment,character-method	plotDimReduce
plotDimReduce,ClusterExperiment,missing-method	plotDimReduce
plotDimReduce,ClusterExperiment,numeric-method	plotDimReduce
plotHeatmap	plotHeatmap
plotHeatmap,ClusterExperiment-method	plotHeatmap
plotHeatmap,data.frame-method	plotHeatmap
plotHeatmap,ExpressionSet-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
requiredArgs	ClusterFunction-methods
requiredArgs,character-method	ClusterFunction-methods
requiredArgs,ClusterFunction-method	ClusterFunction-methods
requiredArgs,factor-method	ClusterFunction-methods
RSEC	RSEC
RSEC,ClusterExperiment-method	RSEC
RSEC,data.frame-method	RSEC
RSEC,matrix-method	RSEC
RSEC,SummarizedExperiment-method	RSEC
RSEC-methods	RSEC
rsecFluidigm	rsecFluidigm
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
subsampleClustering,character-method	subsampleClustering
subsampleClustering,ClusterFunction-method	subsampleClustering
tableClusters	ClusterExperiment-methods
tableClusters,ClusterExperiment,character-method	ClusterExperiment-methods
tableClusters,ClusterExperiment,missing-method	ClusterExperiment-methods
tableClusters,ClusterExperiment,numeric-method	ClusterExperiment-methods
transform	transform
transform,ClusterExperiment-method	transform
transformation	ClusterExperiment-methods
transformation,ClusterExperiment-method	ClusterExperiment-methods
transformation<-	ClusterExperiment-methods
transformation<-,ClusterExperiment,function-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
