GDM                     Accessor function for EMD ground distance
                        matrix
Phemd                   Phemd class
Phemd-methods           Setter function for protein / gene markers
aggregateSamples        Aggregate expression data from all samples
all_expn_data           Single-cell RNA-seq expression data for
                        melanoma samples
all_genes               All genes included in (subsampled) melanoma
                        single-cell RNA-seq expression data
assignCellClusterNearestNode
                        Assign cells to a reference cell subtype
batchIDs                Accessor function for batch ID for each sample
bindSeuratObj           Attach 'seurat' object to 'Phemd' object
celltypeFreqs           Accessor function for cell subtype distribution
                        for each sample
clusterIndividualSamples
                        Computes cell subtype abundances for each
                        sample
compareSamples          Computes EMD distance matrix representing
                        pairwise dissimilarity between samples
createDataObj           Create 'Phemd' object
drawColnames45          Rotates heatmap marker labels 45 degrees
embedCells              Generate Monocle2 embedding
gaussianffLocal         Models expression data using generalized linear
                        model with Gaussian error
generateGDM             Computes ground distance matrix based on cell
                        embedding
getArithmeticCentroids
                        Get arithmetic centroids (coordinates)
getCellYield            Gets cell yield of each sample as a table
getSampleCelltypeFreqs
                        Returns cell subtype distribution for each
                        sample as a table
getSampleHistsByCluster
                        Gets cell subtype frequency histograms for each
                        sample by cluster ID
getSampleSizes          Retrieve single-cell sample sizes
groupSamples            Performs community detection on sample-sample
                        distance matrix
heatmap_genes           Genes to be used when plotting heatmap for
                        melanoma single-cell RNA-seq expression data
identifyCentroids       Identify cluster centroids (cell names)
monocleInfo             Accessor function for stored Monocle object
orderCellsMonocle       Compute Monocle2 cell state and pseudotime
                        assignments
plotCellYield           Plot cell yield of each sample as bar plot
plotEmbeddings          Plots Monocle2 cell embedding plots
plotGroupedSamplesDmap
                        Plot diffusion map embedding of samples based
                        on distance matrix
plotHeatmaps            Plot heatmap of cell subtypes
plotSummaryHistograms   Plots cell subtype frequency histograms
                        summarizing each group of samples
pooledCells             Accessor function for aggregated cells used for
                        cell subtype definition
printClusterAssignments
                        Writes samples to file based on community
                        detection group assignments
rawExpn                 Accessor function for stored multi-sample raw
                        expression data
removeTinySamples       Remove samples with too few cells
retrieveRefClusters     Retrieve reference cell clusters
sNames                  Accessor function for identifiers of all
                        single-cell samples in experiment
selectFeatures          Perform feature selection on aggregated data
selectMarkers           Accessor function for gene/protein markers
                        measured in experiment
selected_genes          Genes to be used when performing clustering and
                        trajectory analyses on melanoma single-cell
                        RNA-seq expression data
seuratInfo              Accessor function for stored Seurat object
                        within Phemd object
snames_data             Sample names for melanoma single-cell RNA-seq
                        expression data
subsampledBool          Accessor function for whether or not cells were
                        subsampled when aggregated for cell subtype
                        analysis
subsampledIdx           Accessor function for aggregated cells used for
                        cell subtype definition
