ClusterExperiment-class
                        Class ClusterExperiment
ClusterExperiment-methods
                        Helper methods for the ClusterExperiment class
ClusterFunction-methods
                        Helper methods for the ClusterFunction class
RSEC                    Resampling-based Sequential Ensemble Clustering
addClusterings          Add clusterings to ClusterExperiment object
assignUnassigned        Assign unassigned samples to nearest cluster
clusterContrasts        Create contrasts for testing DE of a cluster
clusterDendrogram       Accessing and manipulating the dendrograms
clusterExperiment-deprecated
                        Deprecated functions in package
                        'clusterExperiment'
clusterMany             Create a matrix of clustering across values of
                        parameters
clusterSingle           General wrapper method to cluster the data
fluidigmData            Subset of fluidigm data
getBestFeatures         Function for finding best features associated
                        with clusters
getClusterIndex         getClusterIndex
getClusterManyParams,ClusterExperiment-method
                        Get parameter values of clusterMany clusters
getReducedData,ClusterExperiment-method
                        Return matrix from ClusterExperiment with
                        reduced dimensions
internalFunctionCheck   Class ClusterFunction
listBuiltInFunctions    Built in ClusterFunction options
mainClustering          Cluster distance matrix from subsampling
makeConsensus           Find sets of samples that stay together across
                        clusterings
makeDendrogram          Make hierarchy of set of clusters
mergeClusters           Merge clusters based on dendrogram
numericalAsCharacter    Convert numeric values to character that sort
                        correctly
plotBarplot,ClusterExperiment-method
                        Barplot of 1 or 2 clusterings
plotClusters            Visualize cluster assignments across multiple
                        clusterings
plotClustersTable       Plot heatmap of cross-tabs of 2 clusterings
plotClustersWorkflow,ClusterExperiment-method
                        A plot of clusterings specific for clusterMany
                        and workflow visualization
plotContrastHeatmap,ClusterExperiment-method
                        Plot heatmaps showing significant genes per
                        contrast
plotDendrogram,ClusterExperiment-method
                        Plot dendrogram of ClusterExperiment object
plotFeatureBoxplot      Plot boxplot of feature values by cluster
plotFeatureScatter      Plot scatter plot of feature values colored by
                        cluster
plotHeatmap             Heatmap for showing clustering results and more
plotReducedDims         Plot 2-dimensionsal representation with
                        clusters
plottingFunctions       Convert clusterLegend into useful formats
renameClusters          Change assigned names or colors of clusters
rsecFluidigm            Documentation of rsecFluidigm object
search_pairs            Search pairs of samples that co-cluster across
                        subsamples
seqCluster              Program for sequentially clustering, removing
                        cluster, and starting again.
simData                 Simulated data for running examples
subsampleClustering     Cluster subsamples of the data
subset                  Functions to subset ClusterExperiment Objects
transformData           Transform the original data in a
                        ClusterExperiment object
updateObject            Update old ClusterExperiment object to current
                        class definition
workflowClusters        Methods for workflow clusters
