Man pages for Platypus
Single-Cell Immune Repertoire and Gene Expression Analysis
| GEX_cluster_genes | Differentially expressed genes between clusters or data... |
| 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... |
| GEX_dottile_plot | GEX Dottile plots |
| GEX_gene_visualization | Visualization of marker expression in a data set or of... |
| 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... |
| GEX_pairwise_DEGs | Wrapper for calculating pairwise differentially expressed... |
| 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... |
| 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... |
| VDJ_alpha_beta_Vgene_circos | Produces a Circos plot from the VDJ_analyze output. Connects... |
| VDJ_antigen_integrate | Integrates antigen-specific information into the... |
| VDJ_assemble_for_PnP | Ab sequence assembly for recombinant PnP expression |
| VDJ_build | Minimal Version of the VDJ Building Part from... |
| 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... |
| VDJ_clonal_barplot | Function to create stacked barplots to visualize clonal... |
| VDJ_clonal_donut | Circular VDJ expansion plots |
| VDJ_clonal_expansion | Flexible wrapper for clonal expansion barplots by isotype,... |
| VDJ_clonotype | Platypus V3 clonotyping wrapper |
| VDJ_clonotype_v3_w_enclone | Updated clonotyping function based on implications for cells... |
| VDJ_contigs_to_vgm | Formats "VDJ_contigs_annotations.csv" files from cell ranger... |
| 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... |
| VDJ_dynamics | Tracks a specific VDJ column across multiple... |
| VDJ_expand_aberrants | Expand the aberrant cells in a VDJ dataframe by converting... |
| 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... |
| VDJ_GEX_clonotype_clusters_circos | Makes a Circos plot from the VDJ_GEX_integrate output.... |
| 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... |
| VDJ_overlap_heatmap | Wrapper to determine and plot overlap between VDJ features... |
| 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... |
| VDJ_rarefaction | Plots rarefaction curves for species denoted in the... |
| 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... |
| VGM_build | Function to obtain the VGM object by integrating the VDJ and... |
| VGM_expanded_clones | VDJ utility for T/F column for clonal expansion |
| VGM_expand_featurebarcodes | Utility for feature barcode assignment including clonal... |
| VGM_integrate | Utility for VDJ GEX matrix to integrated VDJ and GEX objects... |
