BSPLeaveCenter          Finds N Leaf centers in the data
JaccardSM               Calculates the Jaccard similarity matrix.
MAN                     Creates network alignments using network
                        constructed from subpopulations after PAC
MINetworkPlot_topEdges
                        Plots mutual information network (mrnet
                        algorithm) connection using the parmigene
                        package. Mutual information calculated with
                        infotheo package.
MINetwork_matrix_topEdges
                        Mutual information network connection matrix
                        generation (mrnet algorithm) using the
                        parmigene package. Mutual information
                        calculated with infotheo package.
MINetwork_simplified_topEdges
                        Outputs the vectorized summary of a network
                        based on the number of edges connected to a
                        node
PAC                     Partition Assisted Clustering PAC 1) utilizes
                        dsp or bsp-ll to recursively partition the data
                        space and 2) applies a short round of kmeans
                        style postprocessing to efficiently output
                        clustered labels of data points.
aggregateData           Aggregates results from the clustering and
                        merging step.
annotateClades          Creates annotation matrix for the clades in
                        aggregated format. The matrix contains average
                        signals of each dimension for each clade in
                        each sample
annotationMatrix_withSubpopProp
                        Adds subpopulation proportion for the
                        annotation matrix for the clades
constellationPlot       Makes constellation plot, in which the
                        centroids are clusters are embedded in the
                        t-SNE 2D plane and the cross-sample
                        relationships are plotted as lines connecting
                        related sample clusters (clades).
fmeasure                F-measure Calculation
getAverageSpreadOf2SubpopClades
                        Calculate the (global) average spread of
                        subpopulations in clades with 2 subpopulations
                        on the constellation plot.
getExtraneousCladeSubpopulations
                        Calculates subpopulations in clades (with two
                        or more subpopulations) that are too far away
                        from other subpopulations (within the same
                        clade) on the constellation plot; these far
                        away subpopulations should be pruned away from
                        the original clades.
getRepresentativeNetworks
                        Representative Networks
heatmapInput            Creates the matrix that can be easily plotted
                        with a heatmap function available in an R
                        package
outputNetworks_topEdges_matrix
                        Wrapper to output the mutual information
                        networks for subpopulations with size larger
                        than a desired threshold.
outputRepresentativeNetworks_topEdges
                        Outputs the representative/clade networks
                        (plots and summary vectors) for subpopulations
                        with size larger than a desired threshold.
                        Saves the networks and the data matrices
                        without the smaller subpopulations.
recordWithinClusterSpread
                        Calculates the within cluster spread
refineSubpopulationLabels
                        Refines the subpopulation labels from PAC using
                        network alignment and small subpopulation
                        information. Outputs a new set of files
                        containing the representative labels.
renamePrunedSubpopulations
                        Prune away specified subpopulations in clades
                        that are far away.
runElbowPointAnalysis   Runs elbow point analysis to find the practical
                        optimal number of clades to output. Outputs the
                        average within sample cluster spread for all
                        samples and the elbow point analysis plot with
                        loess line fitted through the results.
samplePass              Run PAC for Specified Samples
