StartracDiversity       Calculate Startrac-based Diversity Indices
addVariable             Adding Variables After combineTCR() or
                        combineBCR()
alluvialClones          Alluvial Plotting for Single-Cell Object
annotateInvariant       Annotate invariant T cells (MAIT or iNKT) in
                        single-cell TCR data
clonalAbundance         Plot the Relative Abundance of Clones
clonalBias              Calculate Clonal Bias Towards a Cluster or
                        Compartment
clonalCluster           Cluster clones by sequence similarity
clonalCompare           Compare Clonal Abundance Across Variables
clonalDiversity         Calculate Clonal Diversity
clonalHomeostasis       Plot Clonal Homeostasis of the Repertoire
clonalLength            Plot the Distribution of Sequence Lengths
clonalNetwork           Visualize Clonal Network in Dimensional
                        Reductions
clonalOccupy            Plot cloneSize by Variable in Single-Cell
                        Objects
clonalOverlap           Examining the clonal overlap between groups or
                        samples
clonalOverlay           Visualize Distribution of Clonal Frequency
clonalProportion        Plot the Clonal Space Occupied by Specific
                        Clones
clonalQuant             Plot Number or Proportions of Clones
clonalRarefaction       Calculate rarefaction based on the abundance of
                        clones
clonalScatter           Scatter Plot Comparing Clones Across Two
                        Samples
clonalSizeDistribution
                        Plot powerTCR Clustering Based on Clonal Size
combineBCR              Combine B Cell Receptor Contig Data
combineExpression       Adding Clonal Information to Single-Cell Object
combineTCR              Combine T Cell Receptor Contig Data
contig_list             A List of Eight Single-cell TCR Sequencing
                        Runs.
createHTOContigList     Deconvolute Contig Information from Multiplexed
                        Experiments
exportClones            Export Clonal Data in Various Formats
getCirclize             Generate Data Frame to Plot Cord Diagram
getContigDoublets       Get Contig Doublets
highlightClones         Highlighting Specific Clones
loadContigs             Load Immune Receptor Sequencing Contigs
percentAA               Plot Relative Amino Acid Composition by
                        Position
percentGeneUsage        Summarizes and Visualizes Gene Usage
percentKmer             Analyze K-mer Motif Composition
positionalEntropy       Examining the Diversity of Amino Acids by
                        Position
positionalProperty      Plot Positional Physicochemical Property
                        Analysis
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()
