APOTCPlot               Various variations of visualizations of clonal
                        expansion post-RunAPOTC
AdjustAPOTC             Adjust the parameters of the APackOfTheClones
                        reduction in a seurat object
RunAPOTC                Run the APackOfTheClones method on a combined
                        Seurat object for downstream visualization of
                        clonal expansion
combined_pbmc           Example Multi-sampled T-cell seurat object with
                        integrated TCR library
containsApotcRun        Check for the existence of an APackOfTheClones
                        run with its run id
countCloneSizes         count the number of clonotype sizes in a seurat
                        object combined with a VDJ library overall or
                        by cluster
deleteApotcData         Delete the results of an APackOfTheClones run
getApotcDataIds         Get all run ids of previous RunAPOTC runs on a
                        seurat object
getLastApotcDataId      Get the object id of the most recent RunAPOTC
                        run on a seurat object
getReductionCentroids   Calculate seurat cluster centroids based on a
                        Dimensional reduction
getSharedClones         Compute a list of clonotypes that are shared
                        between seurat clusters
mergeCloneSizes         Merge a list of Clustered Clonotype Frequency
                        Tables
overlayLegend           overlay a clone size legend on an
                        APackOfTheClones plot
removeLegend            Remove current APackOfTheClones legend
renameApotcRun          Rename an APackOfTheClones run
showCloneHighlight      Highlight specific clones on an
                        APackOfTheClones ggplot
updateApotc             Update APackOfTheClones objects to the latest
                        format
vizAPOTC                Directly visualize clonal expansion of a
                        combined seurat object
