GEX_DEgenes             Wrapper for differential gene expression
                        analysis and plotting
GEX_GSEA                GEX Gene Set Enrichment Analysis and plotting
GEX_cluster_genes       Differentially expressed genes between clusters
                        or data subsets
GEX_cluster_genes_heatmap
                        Heatmap of cluster defining genes
GEX_cluster_membership
                        Cluster membership plots by sample
GEX_coexpression_coefficient
                        Coexpression of selected genes
GEX_dottile_plot        GEX Dottile plots
GEX_gene_visualization
                        Visualization of marker expression in a data
                        set or of predefined genes (B cells, CD4 T
                        cells and CD8 T cells).
GEX_heatmap             Flexible GEX heatmap wrapper
GEX_lineage_trajectories
                        This is a function to infer single cell
                        trajectories and identifying lineage structures
                        on clustered cells. Using the slingshot library
GEX_pairwise_DEGs       Wrapper for calculating pairwise differentially
                        expressed genes
GEX_phenotype           Assignment of cells to phenotypes based on
                        selected markers
GEX_phenotype_per_clone
                        Plotting of GEX phenotype by VDJ clone
GEX_proportions_barplot
                        Plots proportions of a group of cells within a
                        secondary group of cells. E.g. The proportions
                        of samples in seurat clusters, or the
                        proportions of samples in defined cell subtypes
GEX_scatter_coexpression
                        Scatter plot for coexpression of two selected
                        genes
GEX_volcano             Flexible wrapper for GEX volcano plots
PlatypusDB_AIRR_to_VGM
                        AIRR to Platypus V3 VGM compatibility function
PlatypusDB_VGM_to_AIRR
                        Platypus V3 VGM to AIRR compatibility function
PlatypusDB_load_from_disk
                        PlatypusDB utility for import of local datasets
VDJ_GEX_clonotype_clusters_circos
                        Makes a Circos plot from the VDJ_GEX_integrate
                        output. Connects the clonotypes with the
                        corresponding clusters.
VDJ_GEX_matrix          VDJ GEX processing and integration wrapper
VDJ_GEX_overlay_clones
                        Overlay clones on GEX projection
VDJ_GEX_stats           Standalone VDJ and GEX statistics.
VDJ_VJ_usage_circos     Makes a Circos plot from the VDJ_analyze
                        output. Connects the V gene with the
                        corresponding J gene for each clonotype.
VDJ_Vgene_usage         V(D)J gene usage stacked barplots
VDJ_Vgene_usage_barplot
                        V(D)J gene usage barplots
VDJ_Vgene_usage_stacked_barplot
                        V(D)J gene usage stacked barplots
VDJ_abundances          Calculate abundances/counts of specific
                        features for a VDJ dataframe
VDJ_alpha_beta_Vgene_circos
                        Produces a Circos plot from the VDJ_analyze
                        output. Connects the V-alpha with the
                        corresponding V-beta gene for each clonotype.
VDJ_antigen_integrate   Integrates antigen-specific information into
                        the VDJ/VDJ.GEX.matrix[[1]] object
VDJ_assemble_for_PnP    Ab sequence assembly for recombinant PnP
                        expression
VDJ_build               Minimal Version of the VDJ Building Part from
                        VDJ_GEX_matrix() Function
VDJ_call_enclone        (Re)clonotype a VDJ object using cellranger's
                        enclone tool
VDJ_circos              Plots a Circos diagram from an adjacency
                        matrix. Uses the Circlize chordDiagram
                        function. Is called by
                        VDJ_clonotype_clusters_circos(),
                        VDJ_alpha_beta_Vgene_circos() and
                        VDJ_VJ_usage_circos() functions or works on its
                        own when supplied with an adjacency matrix.
VDJ_clonal_barplot      Function to create stacked barplots to
                        visualize clonal expansion per repertoire
                        directly from a VDJ matrix (either from the
                        minimal_VDJ() or VDJ_GEX_matrix())
VDJ_clonal_donut        Circular VDJ expansion plots
VDJ_clonal_expansion    Flexible wrapper for clonal expansion barplots
                        by isotype, GEX cluster etc.
VDJ_clonotype           Platypus V3 clonotyping wrapper
VDJ_clonotype_v3_w_enclone
                        Updated clonotyping function based on
                        implications for cells with different chain
                        numbers than 1 VDJ 1 VJ chains.
VDJ_contigs_to_vgm      Formats "VDJ_contigs_annotations.csv" files
                        from cell ranger to match the VDJ_GEX_matrix
                        output using only cells with 1VDJ and 1VJ chain
VDJ_db_annotate         Wrapper function of VDJ_antigen_integrate
                        function
VDJ_db_load             Load and preprocess a list of antigen-specific
                        databases
VDJ_diversity           Calculates and plots common diversity and
                        overlap measures for repertoires and alike.
                        Requires the vegan package
VDJ_dynamics            Tracks a specific VDJ column across multiple
                        samples/timepoints.
VDJ_expand_aberrants    Expand the aberrant cells in a VDJ dataframe by
                        converting them into additional rows
VDJ_extract_germline_consensus_ref
                        Making the trimmed reference and concatenating
                        fr1-fr4
VDJ_germline            Infer germline from the desired software/caller
VDJ_get_public          Function to get shared/public elements across
                        multiple repertoires
VDJ_kmers               Calculates and plots kmers distributions and
                        frequencies.
VDJ_logoplot_vector     Flexible logoplot wrapper
VDJ_network             Similarity networks based on CDR3 regions
VDJ_ordination          Performs ordination/dimensionality reduction
                        for a species incidence matrix, depending on
                        the species selected in the feature.columns
                        parameter.
VDJ_overlap_heatmap     Wrapper to determine and plot overlap between
                        VDJ features across groups
VDJ_phylogenetic_trees
                        Creates phylogenetic trees from a VDJ dataframe
VDJ_phylogenetic_trees_plot
                        Phylogenetic tree plotting
VDJ_plot_SHM            Plotting of somatic hypermutation counts
VDJ_public              Function to get shared/public elements across
                        multiple repertoires
VDJ_rarefaction         Plots rarefaction curves for species denoted in
                        the feature.columns parameter across groups
                        determined by grouping.columns
VDJ_variants_per_clone
                        Wrapper for variant analysis by clone
VGM_build               Function to obtain the VGM object by
                        integrating the VDJ and GEX/Seurat objects
VGM_expand_featurebarcodes
                        Utility for feature barcode assignment
                        including clonal information
VGM_expanded_clones     VDJ utility for T/F column for clonal expansion
VGM_integrate           Utility for VDJ GEX matrix to integrated VDJ
                        and GEX objects after addition of data to
                        either
small_vdj               Small VDJ dataframe for function testing
                        purposes
small_vgm               Small VDJ GEX matrix (VGM) for function testing
                        purposes
