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
addClusters,ClusterExperiment,matrix-method
                        Functions to add/remove clusters to
                        ClusterExperiment
clusterContrasts,ClusterExperiment-method
                        Create contrasts for testing DE of a cluster
clusterMany,matrix-method
                        Create a matrix of clustering across values of
                        parameters
clusterSingle           General wrapper method to cluster the data
combineMany,matrix,missing-method
                        Find sets of samples that stay together across
                        clusterings
getBestFeatures,matrix-method
                        Function for finding best features associated
                        with clusters
getClusterManyParams,ClusterExperiment-method
                        Get parameter values of clusterMany clusters
internalFunctionCheck   Class ClusterFunction
listBuiltInFunctions    Built in ClusterFunction options
mainClustering          Cluster distance matrix from subsampling
makeDendrogram          Make hierarchy of set of clusters
mergeClusters,matrix-method
                        Merge clusters based on dendrogram
plotBarplot,ClusterExperiment,character-method
                        Barplot of 1 or 2 clusterings
plotClusters,ClusterExperiment,character-method
                        Visualize cluster assignments across multiple
                        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
plotDimReduce,ClusterExperiment,character-method
                        Plot 2-dimensionsal representation with
                        clusters
plotHeatmap,SummarizedExperiment-method
                        Heatmap for showing clustering results and more
plottingFunctions       Convert clusterLegend into useful formats
rsecFluidigm            RSEC run for vignette
seqCluster              Program for sequentially clustering, removing
                        cluster, and starting again.
simData                 Simulated data for running examples
subsampleClustering     Cluster subsamples of the data
transform               Transform the original data in a
                        ClusterExperiment object
workflowClusters        Methods for workflow clusters
