StartracDiversity       Startrac-based diversity indices for
                        single-cell RNA-seq
addVariable             Adding variables after combineTCR() or
                        combineBCR()
alluvialClones          Alluvial plotting for single-cell object meta
                        data
clonalAbundance         Demonstrate the relative abundance of clones by
                        group or sample
clonalBias              Examine skew of clones towards a cluster or
                        compartment
clonalCluster           Clustering adaptive receptor sequences by edit
                        distance
clonalCompare           Demonstrate the difference in clonal
                        proportions / counts between clones
clonalDiversity         Calculate the clonal diversity for samples or
                        groupings
clonalHomeostasis       Examining the clonal homeostasis of the
                        repertoire
clonalLength            Demonstrate the distribution of clonal length
clonalNetwork           Visualize clonal network along reduced
                        dimensions
clonalOccupy            Visualize the number of single cells with
                        cloneSizes by cluster
clonalOverlap           Examining the clonal overlap between groups or
                        samples
clonalOverlay           Visualize distribution of clonal frequency
                        overlaid on dimensional reduction plots
clonalProportion        Examining the clonal space occupied by specific
                        clones
clonalQuant             Quantify the unique clones by group or sample
clonalRarefaction       Calculate rarefaction based on the abundance of
                        clones
clonalScatter           Scatter plot comparing the clonal expansion of
                        two samples
clonalSizeDistribution
                        Hierarchical clustering of clones using
                        Gamma-GPD spliced threshold model
combineBCR              Combining the list of B cell receptor contigs
                        into clones
combineExpression       Adding clone information to a single-cell
                        object
combineTCR              Combining the list of T cell receptor contigs
                        into clones
contig_list             A list of 8 single-cell T cell receptor
                        sequences runs.
createHTOContigList     Generate a contig list from a multiplexed
                        experiment
exportClones            Exporting clones
getCirclize             Generate data frame to be used with circlize R
                        package to visualize clones as a chord diagram.
getContigDoublets       Get Contig Doublets
highlightClones         Highlighting specific clones in Seurat
loadContigs             Loading the contigs derived from single-cell
                        sequencing
mini_contig_list        Processed subset of 'contig_list'
percentAA               Examining the relative amino acid composition
                        by position
percentGenes            Examining the VDJ gene usage across clones
percentKmer             Examining the relative composition of kmer
                        motifs in clones.
percentVJ               Quantifying the V and J gene usage across
                        clones
positionalEntropy       Examining the diversity of amino acids by
                        position
positionalProperty      Examining the mean property of amino acids by
                        position
quietVDJgenes           Remove TCR and BCR genes from variable gene
                        results
scRep_example           A Seurat object of 500 single T cells,
subsetClones            Subset the product of combineTCR() or
                        combineBCR()
vizGenes                Visualizing the distribution of gene usage
