Startrac                The Startrac Class
StartracDiversity       Diversity indices for single-cell RNA-seq
abundanceContig         Demonstrate the relative abundance of
                        clonotypes by group or sample.
addVariable             Adding variables after the combination of
                        contigs.
alluvialClonotypes      Exploring interaction of clonotypes by seurat
                        or SCE dynamics
clonalDiversity         Examine the clonal diversity of samples
clonalHomeostasis       Examining the clonal homeostasis
clonalOverlap           Examining the clonal overlap between groups or
                        samples
clonalProportion        Examining the clonal space occupied by specific
                        clonotypes
clonesizeDistribution   Hierarchical clustering of clonotypes on
                        clonotype size and Jensen-Shannon divergence
combineBCR              Combining the list of B Cell Receptor contigs
combineExpression       Adding clonotype information to a seurat or SCE
                        object
combineTCR              Combining the list of T Cell Receptor contigs
compareClonotypes       Demonstrate the difference in clonal proportion
                        between clonotypes
contig_list             A data set of T cell contigs as a list outputed
                        from the filter_contig_annotation files.
expression2List         Allows users to take the meta data in
                        seurat/SCE and place it into a list that will
                        work with all the functions
getCirclize             Generate data frame to be used with circlize R
                        package to visualize clonotypes as a chord
                        diagram.
highlightClonotypes     Highlighting specific clonotypes in Seurat
lengthContig            Demonstrate the distribution of lengths
                        filtered contigs.
occupiedscRepertoire    Visualize the number of single cells with
                        clonotype frequencies by cluster
quantContig             Quantify the unique clonotypes in the filtered
                        contigs.
screp_example           A seurat object of 1000 single T cells derived
                        from 3 clear cell renal carcinoma patients.
stripBarcode            Removing any additional prefixes to the
                        barcodes of filtered contigs.
subsetContig            Subset the product of combineTCR() combineBCR()
                        or expression2List()
vizVgenes               Visualizing the distribution of TCR V gene
                        usage
