# Compare Clusterings for Single-Cell Sequencing

## Documentation for package ‘clusterExperiment’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D G I L M N O P R S T W misc

## -- A --

addClusters | Functions to add/remove clusters to ClusterExperiment
addClusters-method | Functions to add/remove clusters to ClusterExperiment
algorithmType | Helper methods for the ClusterFunction class
algorithmType-method | Helper methods for the ClusterFunction class

## -- B --

bigPalette | Convert clusterLegend into useful formats

## -- C --

clusterContrasts | Create contrasts for testing DE of a cluster
clusterContrasts-method | Create contrasts for testing DE of a cluster
ClusterExperiment | Class ClusterExperiment
clusterExperiment | Class ClusterExperiment
ClusterExperiment-class | Class ClusterExperiment
clusterExperiment-method | Class ClusterExperiment
ClusterExperiment-methods | Helper methods for the ClusterExperiment class
ClusterFunction | Class ClusterFunction
clusterFunction | Class ClusterFunction
ClusterFunction-class | Class ClusterFunction
clusterFunction-method | Class ClusterFunction
ClusterFunction-methods | Helper methods for the ClusterFunction class
clusterInfo | Helper methods for the ClusterExperiment class
clusterInfo-method | Helper methods for the ClusterExperiment class
clusterLabels | Helper methods for the ClusterExperiment class
clusterLabels-method | Helper methods for the ClusterExperiment class
clusterLabels<- | Helper methods for the ClusterExperiment class
clusterLabels<--method | Helper methods for the ClusterExperiment class
clusterLegend | Helper methods for the ClusterExperiment class
clusterLegend-method | Helper methods for the ClusterExperiment class
clusterLegend<- | Helper methods for the ClusterExperiment class
clusterLegend<--method | Helper methods for the ClusterExperiment class
clusterMany | Create a matrix of clustering across values of parameters
clusterMany-method | Create a matrix of clustering across values of parameters
clusterMatrix | Helper methods for the ClusterExperiment class
clusterMatrix-method | Helper methods for the ClusterExperiment class
clusterMatrixNamed | Helper methods for the ClusterExperiment class
clusterMatrixNamed-method | Helper methods for the ClusterExperiment class
clusterSingle | General wrapper method to cluster the data
clusterSingle-method | General wrapper method to cluster the data
clusterTypes | Helper methods for the ClusterExperiment class
clusterTypes-method | Helper methods for the ClusterExperiment class
clusterTypes<- | Helper methods for the ClusterExperiment class
clusterTypes<--method | Helper methods for the ClusterExperiment class
coClustering | Helper methods for the ClusterExperiment class
coClustering-method | Helper methods for the ClusterExperiment class
coClustering<- | Helper methods for the ClusterExperiment class
coClustering<--method | Helper methods for the ClusterExperiment class
combineMany | Find sets of samples that stay together across clusterings
combineMany-method | Find sets of samples that stay together across clusterings
convertClusterLegend | Convert clusterLegend into useful formats
convertClusterLegend-method | Convert clusterLegend into useful formats

## -- D --

dendroClusterIndex | Helper methods for the ClusterExperiment class
dendroClusterIndex-method | Helper methods for the ClusterExperiment class

## -- G --

getBestFeatures | Function for finding best features associated with clusters
getBestFeatures-method | Function for finding best features associated with clusters
getBuiltInFunction | Built in ClusterFunction options
getBuiltInFunction-method | Built in ClusterFunction options
getClusterManyParams | Get parameter values of clusterMany clusters
getClusterManyParams-method | Get parameter values of clusterMany clusters
getMergeCorrespond | Merge clusters based on dendrogram
getMergeCorrespond-method | Merge clusters based on dendrogram
getPostProcessingArgs | Cluster distance matrix from subsampling
getPostProcessingArgs-method | Cluster distance matrix from subsampling

## -- I --

inputType | Helper methods for the ClusterFunction class
inputType-method | Helper methods for the ClusterFunction class
internalFunctionCheck | Class ClusterFunction

## -- L --

listBuiltInFunctions | Built in ClusterFunction options
listBuiltInType01 | Built in ClusterFunction options
listBuiltInTypeK | Built in ClusterFunction options

## -- M --

mainClustering | Cluster distance matrix from subsampling
mainClustering-method | Cluster distance matrix from subsampling
makeBlankData | Convert clusterLegend into useful formats
makeDendrogram | Make hierarchy of set of clusters
makeDendrogram-method | Make hierarchy of set of clusters
mergeClusterIndex | Merge clusters based on dendrogram
mergeClusterIndex-method | Merge clusters based on dendrogram
mergeClusters | Merge clusters based on dendrogram
mergeClusters-method | Merge clusters based on dendrogram
mergeCutoff | Merge clusters based on dendrogram
mergeCutoff-method | Merge clusters based on dendrogram
mergeMethod | Merge clusters based on dendrogram
mergeMethod-method | Merge clusters based on dendrogram

## -- N --

nClusters | Helper methods for the ClusterExperiment class
nClusters-method | Helper methods for the ClusterExperiment class
nFeatures | Helper methods for the ClusterExperiment class
nFeatures-method | Helper methods for the ClusterExperiment class
nodeMergeInfo | Merge clusters based on dendrogram
nodeMergeInfo-method | Merge clusters based on dendrogram
nSamples | Helper methods for the ClusterExperiment class
nSamples-method | Helper methods for the ClusterExperiment class

## -- O --

orderSamples | Helper methods for the ClusterExperiment class
orderSamples-method | Helper methods for the ClusterExperiment class
orderSamples<- | Helper methods for the ClusterExperiment class
orderSamples<--method | Helper methods for the ClusterExperiment class

## -- P --

plotBarplot | Barplot of 1 or 2 clusterings
plotBarplot-method | Barplot of 1 or 2 clusterings
plotClusters | Visualize cluster assignments across multiple clusterings
plotClusters-method | Visualize cluster assignments across multiple clusterings
plotClustersWorkflow | A plot of clusterings specific for clusterMany and workflow visualization
plotClustersWorkflow-method | A plot of clusterings specific for clusterMany and workflow visualization
plotCoClustering | Heatmap for showing clustering results and more
plotCoClustering-method | Heatmap for showing clustering results and more
plotContrastHeatmap | Plot heatmaps showing significant genes per contrast
plotContrastHeatmap-method | Plot heatmaps showing significant genes per contrast
plotDendrogram | Plot dendrogram of clusterExperiment object
plotDendrogram-method | Plot dendrogram of clusterExperiment object
plotDimReduce | Plot 2-dimensionsal representation with clusters
plotDimReduce-method | Plot 2-dimensionsal representation with clusters
plotHeatmap | Heatmap for showing clustering results and more
plotHeatmap-method | Heatmap for showing clustering results and more
plottingFunctions | Convert clusterLegend into useful formats
primaryCluster | Helper methods for the ClusterExperiment class
primaryCluster-method | Helper methods for the ClusterExperiment class
primaryClusterIndex | Helper methods for the ClusterExperiment class
primaryClusterIndex-method | Helper methods for the ClusterExperiment class
primaryClusterIndex<- | Helper methods for the ClusterExperiment class
primaryClusterIndex<--method | Helper methods for the ClusterExperiment class
primaryClusterNamed | Helper methods for the ClusterExperiment class
primaryClusterNamed-method | Helper methods for the ClusterExperiment class

## -- R --

removeClusters | Functions to add/remove clusters to ClusterExperiment
removeClusters-method | Functions to add/remove clusters to ClusterExperiment
removeUnclustered | Functions to add/remove clusters to ClusterExperiment
removeUnclustered-method | Functions to add/remove clusters to ClusterExperiment
requiredArgs | Helper methods for the ClusterFunction class
requiredArgs-method | Helper methods for the ClusterFunction class
RSEC | Resampling-based Sequential Ensemble Clustering
RSEC-method | Resampling-based Sequential Ensemble Clustering
RSEC-methods | Resampling-based Sequential Ensemble Clustering
rsecFluidigm | RSEC run for vignette

## -- S --

seqCluster | Program for sequentially clustering, removing cluster, and starting again.
seqPal1 | Convert clusterLegend into useful formats
seqPal2 | Convert clusterLegend into useful formats
seqPal3 | Convert clusterLegend into useful formats
seqPal4 | Convert clusterLegend into useful formats
seqPal5 | Convert clusterLegend into useful formats
setBreaks | Convert clusterLegend into useful formats
setToCurrent | Methods for workflow clusters
setToCurrent-method | Methods for workflow clusters
setToFinal | Methods for workflow clusters
setToFinal-method | Methods for workflow clusters
show-method | Helper methods for the ClusterExperiment class
showBigPalette | Convert clusterLegend into useful formats
showHeatmapPalettes | Convert clusterLegend into useful formats
simCount | Simulated data for running examples
simData | Simulated data for running examples
subsampleClustering | Cluster subsamples of the data
subsampleClustering-method | Cluster subsamples of the data

## -- T --

tableClusters | Helper methods for the ClusterExperiment class
tableClusters-method | Helper methods for the ClusterExperiment class
transform | Transform the original data in a ClusterExperiment object
transform-method | Transform the original data in a ClusterExperiment object
transformation | Helper methods for the ClusterExperiment class
transformation-method | Helper methods for the ClusterExperiment class
transformation<- | Helper methods for the ClusterExperiment class
transformation<--method | Helper methods for the ClusterExperiment class
trueCluster | Simulated data for running examples

## -- W --

workflowClusterDetails | Methods for workflow clusters
workflowClusterDetails-method | Methods for workflow clusters
workflowClusters | Methods for workflow clusters
workflowClusters-method | Methods for workflow clusters
workflowClusterTable | Methods for workflow clusters
workflowClusterTable-method | Methods for workflow clusters

## -- misc --

[-method | Helper methods for the ClusterExperiment class