| 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_DEgenes | Wrapper for differential gene expression analysis and plotting |
| 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_GSEA | GEX Gene Set Enrichment Analysis and plotting |
| 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_load_from_disk | PlatypusDB utility for import of local datasets |
| PlatypusDB_VGM_to_AIRR | Platypus V3 VGM to AIRR compatibility function |
| small_vdj | Small VDJ dataframe for function testing purposes |
| small_vgm | Small VDJ GEX matrix (VGM) for function testing purposes |
| 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_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_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 |
| 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_VJ_usage_circos | Makes a Circos plot from the VDJ_analyze output. Connects the V gene with the corresponding J gene for each clonotype. |
| VGM_build | Function to obtain the VGM object by integrating the VDJ and GEX/Seurat objects |
| VGM_expanded_clones | VDJ utility for T/F column for clonal expansion |
| VGM_expand_featurebarcodes | Utility for feature barcode assignment including clonal information |
| VGM_integrate | Utility for VDJ GEX matrix to integrated VDJ and GEX objects after addition of data to either |