# Compare Clusterings for Single-Cell Sequencing

## Documentation for package ‘clusterExperiment’ version 1.2.0

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

## Help Pages

A B C G 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

## -- B --

bigPalette | Various functions useful for plotting

## -- C --

cluster01 | Cluster distance matrix from subsampling
clusterContrasts | Create contrasts for testing DE of a cluster
clusterContrasts-method | Create contrasts for testing DE of a cluster
clusterD | Cluster distance matrix from subsampling
ClusterExperiment | Class ClusterExperiment
clusterExperiment | Class ClusterExperiment
ClusterExperiment-class | Class ClusterExperiment
clusterExperiment-method | Class ClusterExperiment
ClusterExperiment-methods | Helper methods for the ClusterExperiment class
clusterInfo | Helper methods for the ClusterExperiment class
clusterInfo-method | Helper methods for the ClusterExperiment class
clusterK | Cluster distance matrix from subsampling
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
clusterSingle-methods | 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

## -- G --

getBestFeatures | Function for finding best features associated with clusters
getBestFeatures-method | Function for finding best features associated with clusters

## -- M --

makeBlankData | Various functions useful for plotting
makeDendrogram | Make hierarchy of set of clusters
makeDendrogram-method | Make hierarchy of set of clusters
mergeClusters | Merge clusters based on dendrogram
mergeClusters-method | Merge clusters based on dendrogram

## -- N --

nClusters | Helper methods for the ClusterExperiment class
nClusters-method | Helper methods for the ClusterExperiment class
nFeatures | Generic function that returns the number of features
nFeatures-method | Helper methods for the ClusterExperiment class
nSamples | Generic function that returns the number of samples
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 --

plotClusters | Visualize cluster assignments across multiple clusterings
plotClusters-method | Visualize cluster assignments across multiple clusterings
plotCoClustering | Heatmap for showing clustering results and more
plotCoClustering-method | Heatmap for showing clustering results and more
plotDendrogram | Make hierarchy of set of clusters
plotDendrogram-method | Make hierarchy of set of clusters
plotHeatmap | Heatmap for showing clustering results and more
plotHeatmap-method | Heatmap for showing clustering results and more
plottingFunctions | Various functions useful for plotting
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
RSEC | Resampling-based Sequential Ensemble Clustering
RSEC-method | Resampling-based Sequential Ensemble Clustering
RSEC-methods | Resampling-based Sequential Ensemble Clustering

## -- S --

seqCluster | Program for sequentially clustering, removing cluster, and starting again.
seqPal1 | Various functions useful for plotting
seqPal2 | Various functions useful for plotting
seqPal3 | Various functions useful for plotting
seqPal4 | Various functions useful for plotting
seqPal5 | Various functions useful for plotting
setBreaks | Various functions useful for plotting
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 | Various functions useful for plotting
showHeatmapPalettes | Various functions useful for plotting
simCount | Simulated data for running examples
simData | Simulated data for running examples
subsampleClustering | Cluster subsamples of the data

## -- T --

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
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