addClusterings	addClusterings
addClusterings,ClusterExperiment,ClusterExperiment-method	addClusterings
addClusterings,ClusterExperiment,matrix-method	addClusterings
addClusterings,ClusterExperiment,vector-method	addClusterings
addToColData	ClusterExperiment-methods
addToColData,ClusterExperiment-method	ClusterExperiment-methods
algorithmType	ClusterFunction-methods
algorithmType,character-method	ClusterFunction-methods
algorithmType,ClusterFunction-method	ClusterFunction-methods
algorithmType,factor-method	ClusterFunction-methods
algorithmType,list-method	ClusterFunction-methods
assignUnassigned	assignUnassigned
assignUnassigned,ClusterExperiment-method	assignUnassigned
bigPalette	plottingFunctions
bubblePlot,table,table-method	plotClustersTable
checkDendrogram	clusterDendrogram
checkDendrogram,ClusterExperiment,phylo4d,phylo4d-method	clusterDendrogram
clusterContrasts	clusterContrasts
clusterContrasts,ClusterExperiment-method	clusterContrasts
clusterContrasts,vector-method	clusterContrasts
clusterDendrogram	clusterDendrogram
clusterDendrogram,ClusterExperiment-method	clusterDendrogram
ClusterExperiment	ClusterExperiment-class
ClusterExperiment,matrixOrHDF5,ANY-method	ClusterExperiment-class
ClusterExperiment,SingleCellExperiment,character-method	ClusterExperiment-class
ClusterExperiment,SingleCellExperiment,factor-method	ClusterExperiment-class
ClusterExperiment,SingleCellExperiment,matrix-method	ClusterExperiment-class
ClusterExperiment,SingleCellExperiment,numeric-method	ClusterExperiment-class
ClusterExperiment,SummarizedExperiment,ANY-method	ClusterExperiment-class
ClusterExperiment-class	ClusterExperiment-class
clusterExperiment-deprecated	clusterExperiment-deprecated
ClusterExperiment-methods	ClusterExperiment-methods
ClusterFunction	ClusterFunction-class
ClusterFunction,function-method	ClusterFunction-class
ClusterFunction-class	ClusterFunction-class
ClusterFunction-methods	ClusterFunction-methods
clusteringInfo	ClusterExperiment-methods
clusteringInfo,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,matrixOrHDF5-method	clusterMany
clusterMany,SingleCellExperiment-method	clusterMany
clusterMany,SummarizedExperiment-method	clusterMany
clusterMatrix	ClusterExperiment-methods
clusterMatrix,ClusterExperiment-method	ClusterExperiment-methods
clusterMatrixColors	ClusterExperiment-methods
clusterMatrixColors,ClusterExperiment-method	ClusterExperiment-methods
clusterMatrixNamed	ClusterExperiment-methods
clusterMatrixNamed,ClusterExperiment-method	ClusterExperiment-methods
clusterSingle	clusterSingle
clusterSingle,ClusterExperiment,missing-method	clusterSingle
clusterSingle,matrixOrHDF5OrNULL,matrixOrNULL-method	clusterSingle
clusterSingle,matrixOrHDF5OrNULL,missing-method	clusterSingle
clusterSingle,missing,matrixOrNULL-method	clusterSingle
clusterSingle,SingleCellExperiment,missing-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,dsCMatrix-method	ClusterExperiment-methods
coClustering<-,ClusterExperiment,matrix-method	ClusterExperiment-methods
colDataClusters	ClusterExperiment-methods
colDataClusters,ClusterExperiment-method	ClusterExperiment-methods
combineMany	clusterExperiment-deprecated
combineMany,ANY-method	clusterExperiment-deprecated
convertClusterLegend	plottingFunctions
convertClusterLegend,ClusterExperiment-method	plottingFunctions
convertToDendrogram	clusterDendrogram
convertToDendrogram,ClusterExperiment-method	clusterDendrogram
defaultNDims	reduceFunctions
defaultNDims,matrixOrHDF5-method	reduceFunctions
defaultNDims,SingleCellExperiment-method	reduceFunctions
dendroClusterIndex	ClusterExperiment-methods
dendroClusterIndex,ClusterExperiment-method	ClusterExperiment-methods
eraseMergeInfo	mergeClusters
eraseMergeInfo,ClusterExperiment-method	mergeClusters
filterData	reduceFunctions
filterData,SummarizedExperiment-method	reduceFunctions
filterNames	reduceFunctions
filterNames,SummarizedExperiment-method	reduceFunctions
getBestFeatures	getBestFeatures
getBestFeatures,ClusterExperiment-method	getBestFeatures
getBestFeatures,matrixOrHDF5-method	getBestFeatures
getBuiltInFunction	builtInClusteringFunctions
getBuiltInFunction,character-method	builtInClusteringFunctions
getClusterIndex	getClusterIndex
getClusterIndex,ClusterExperiment-method	getClusterIndex
getClusterManyParams	getClusterManyParams
getClusterManyParams,ClusterExperiment-method	getClusterManyParams
getMergeCorrespond	mergeClusters
getMergeCorrespond,ClusterExperiment-method	mergeClusters
getPostProcessingArgs	mainClustering
getPostProcessingArgs,ClusterFunction-method	mainClustering
getReducedData	reduceFunctions
getReducedData,ClusterExperiment-method	reduceFunctions
getSingleClusterIndex	getClusterIndex
getSingleClusterIndex,ClusterExperiment-method	getClusterIndex
inputType	ClusterFunction-methods
inputType,character-method	ClusterFunction-methods
inputType,ClusterFunction-method	ClusterFunction-methods
inputType,factor-method	ClusterFunction-methods
inputType,list-method	ClusterFunction-methods
internalFunctionCheck	ClusterFunction-class
listBuiltInFilterStats	reduceFunctions
listBuiltInFunctions	builtInClusteringFunctions
listBuiltInReducedDims	reduceFunctions
listBuiltInType01	builtInClusteringFunctions
listBuiltInTypeK	builtInClusteringFunctions
mainClustering	mainClustering
mainClustering,character-method	mainClustering
mainClustering,ClusterFunction-method	mainClustering
makeBlankData	plottingFunctions
makeConsensus	makeConsensus
makeConsensus,ClusterExperiment-method	makeConsensus
makeConsensus,matrix-method	makeConsensus
makeDendrogram	makeDendrogram
makeDendrogram,ClusterExperiment-method	makeDendrogram
makeDendrogram,dist-method	makeDendrogram
makeDendrogram,matrixOrHDF5-method	makeDendrogram
makeFilterStats	reduceFunctions
makeFilterStats,ClusterExperiment-method	reduceFunctions
makeFilterStats,matrixOrHDF5-method	reduceFunctions
makeFilterStats,SummarizedExperiment-method	reduceFunctions
makeReducedDims	reduceFunctions
makeReducedDims,ClusterExperiment-method	reduceFunctions
makeReducedDims,matrixOrHDF5-method	reduceFunctions
makeReducedDims,SingleCellExperiment-method	reduceFunctions
makeReducedDims,SummarizedExperiment-method	reduceFunctions
massivePalette	plottingFunctions
mergeClusterIndex	mergeClusters
mergeClusterIndex,ClusterExperiment-method	mergeClusters
mergeClusters	mergeClusters
mergeClusters,ClusterExperiment-method	mergeClusters
mergeClusters,matrixOrHDF5-method	mergeClusters
mergeCutoff	mergeClusters
mergeCutoff,ClusterExperiment-method	mergeClusters
mergeMethod	mergeClusters
mergeMethod,ClusterExperiment-method	mergeClusters
nClusterings	ClusterExperiment-methods
nClusterings,ClusterExperiment-method	ClusterExperiment-methods
nClusters	ClusterExperiment-methods
nClusters,ClusterExperiment-method	ClusterExperiment-methods
nFeatures	ClusterExperiment-methods
nFeatures,ClusterExperiment-method	ClusterExperiment-methods
nInternalNodes	clusterDendrogram
nInternalNodes,ClusterExperiment-method	clusterDendrogram
nNodes	clusterDendrogram
nNodes,ClusterExperiment-method	clusterDendrogram
nodeIds	clusterDendrogram
nodeIds,ClusterExperiment-method	clusterDendrogram
nodeLabels	clusterDendrogram
nodeLabels,ClusterExperiment-method	clusterDendrogram
nodeLabels<-	clusterDendrogram
nodeLabels<-,ClusterExperiment-method	clusterDendrogram
nodeMergeInfo	mergeClusters
nodeMergeInfo,ClusterExperiment-method	mergeClusters
nSamples	ClusterExperiment-methods
nSamples,ClusterExperiment-method	ClusterExperiment-methods
nTips	clusterDendrogram
nTips,ClusterExperiment-method	clusterDendrogram
numericalAsCharacter	numericalAsCharacter
orderSamples	ClusterExperiment-methods
orderSamples,ClusterExperiment-method	ClusterExperiment-methods
orderSamples<-	ClusterExperiment-methods
orderSamples<-,ClusterExperiment,numeric-method	ClusterExperiment-methods
plotBarplot	plotBarplot
plotBarplot,ClusterExperiment-method	plotBarplot
plotBarplot,matrix-method	plotBarplot
plotBarplot,vector-method	plotBarplot
plotClusterLegend	plottingFunctions
plotClusterLegend,ClusterExperiment-method	plottingFunctions
plotClusters	plotClusters
plotClusters,ClusterExperiment-method	plotClusters
plotClusters,matrix-method	plotClusters
plotClustersTable	plotClustersTable
plotClustersTable,ClusterExperiment-method	plotClustersTable
plotClustersTable,table-method	plotClustersTable
plotClustersWorkflow	plotClustersWorkflow
plotClustersWorkflow,ClusterExperiment-method	plotClustersWorkflow
plotCoClustering	plotHeatmap
plotCoClustering,ClusterExperiment-method	plotHeatmap
plotContrastHeatmap	plotContrastHeatmap
plotContrastHeatmap,ClusterExperiment-method	plotContrastHeatmap
plotDendrogram	plotDendrogram
plotDendrogram,ClusterExperiment-method	plotDendrogram
plotFeatureBoxplot	plotFeatureBoxplot
plotFeatureBoxplot,ClusterExperiment,character-method	plotFeatureBoxplot
plotFeatureBoxplot,ClusterExperiment,numeric-method	plotFeatureBoxplot
plotFeatureScatter	plotFeatureScatter
plotFeatureScatter,ClusterExperiment,character-method	plotFeatureScatter
plotFeatureScatter,ClusterExperiment,numeric-method	plotFeatureScatter
plotHeatmap	plotHeatmap
plotHeatmap,ClusterExperiment-method	plotHeatmap
plotHeatmap,data.frame-method	plotHeatmap
plotHeatmap,ExpressionSet-method	plotHeatmap
plotHeatmap,matrixOrHDF5-method	plotHeatmap
plotHeatmap,SingleCellExperiment-method	plotHeatmap
plotHeatmap,SummarizedExperiment-method	plotHeatmap
plotHeatmap,table-method	plotHeatmap
plotReducedDims	plotReducedDims
plotReducedDims,ClusterExperiment-method	plotReducedDims
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
primaryClusterLabel	ClusterExperiment-methods
primaryClusterLabel,ClusterExperiment-method	ClusterExperiment-methods
primaryClusterNamed	ClusterExperiment-methods
primaryClusterNamed,ClusterExperiment-method	ClusterExperiment-methods
primaryClusterType	ClusterExperiment-methods
primaryClusterType,ClusterExperiment-method	ClusterExperiment-methods
recolorClusters	renameClusters
recolorClusters,ClusterExperiment,character-method	renameClusters
reduceFunctions	reduceFunctions
removeClusterings	addClusterings
removeClusterings,ClusterExperiment-method	subset
removeClusters	subset
removeClusters,ClusterExperiment-method	subset
removeUnassigned	assignUnassigned
removeUnassigned,ClusterExperiment-method	assignUnassigned
renameClusters	renameClusters
renameClusters,ClusterExperiment,character-method	renameClusters
requiredArgs	ClusterFunction-methods
requiredArgs,character-method	ClusterFunction-methods
requiredArgs,ClusterFunction-method	ClusterFunction-methods
requiredArgs,factor-method	ClusterFunction-methods
requiredArgs,list-method	ClusterFunction-methods
RSEC	RSEC
RSEC,ClusterExperiment-method	RSEC
RSEC,data.frame-method	RSEC
RSEC,matrix-method	RSEC
RSEC,matrixOrHDF5-method	RSEC
RSEC,SingleCellExperiment-method	RSEC
RSEC,SummarizedExperiment-method	RSEC
RSEC-methods	RSEC
rsecFluidigm	rsecFluidigm
sampleDendrogram	clusterDendrogram
sampleDendrogram,ClusterExperiment-method	clusterDendrogram
search_pairs	search_pairs
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-methods
show,ClusterExperiment-method	ClusterExperiment-methods
showHeatmapPalettes	plottingFunctions
showPalette	plottingFunctions
simCount	simData
simData	simData
subsampleClustering	subsampleClustering
subsampleClustering,character-method	subsampleClustering
subsampleClustering,ClusterFunction-method	subsampleClustering
subset	subset
subsetByCluster	subset
subsetByCluster,ClusterExperiment-method	subset
tableClusters	plotClustersTable
tableClusters,ClusterExperiment-method	plotClustersTable
transformation	ClusterExperiment-methods
transformation,ClusterExperiment-method	ClusterExperiment-methods
transformation<-	ClusterExperiment-methods
transformation<-,ClusterExperiment,function-method	ClusterExperiment-methods
transformData	transformData
transformData,ClusterExperiment-method	transformData
transformData,matrixOrHDF5-method	transformData
transformData,SingleCellExperiment-method	transformData
transformData,SummarizedExperiment-method	transformData
trueCluster	simData
updateObject	updateObject
updateObject,ClusterExperiment-method	updateObject
workflowClusterDetails	workflowClusters
workflowClusterDetails,ClusterExperiment-method	workflowClusters
workflowClusters	workflowClusters
workflowClusters,ClusterExperiment-method	workflowClusters
workflowClusterTable	workflowClusters
workflowClusterTable,ClusterExperiment-method	workflowClusters
[,ClusterExperiment,ANY,ANY,ANY-method	subset
[,ClusterExperiment,ANY,character,ANY-method	subset
[,ClusterExperiment,ANY,logical,ANY-method	subset
[,ClusterExperiment,ANY,numeric,ANY-method	subset
