API for Platypus
Single-Cell Immune Repertoire and Gene Expression Analysis
| Global functions | |
|---|---|
| .ADD.BARCODE | Source code |
| .ADD_EDGE_WEIGHTS | Source code |
| .ADJ_MAT | Source code |
| .AVERAGE_DAUGHTERS | Source code |
| .AVERAGE_ISOTYPES | Source code |
| .Arg_base | Source code |
| .Arg_onehot | Source code |
| .CELL.DIVISION.LINEAR | Source code |
| .CELL.DIVISION.LINEAR.INVERSE | Source code |
| .CENTRALITY_METRICS | Source code |
| .CLONAL_FREQUENCY_EDGES_FROM_GERM | Source code |
| .CLONAL_FREQUENCY_PATH_FROM_GERM | Source code |
| .CLUSTER_COEFFICIENTS | Source code |
| .COLOR_PATH | Source code |
| .COUNT_DATA_INFO | Source code |
| .COUNT_ELEMENTS | Source code |
| .CREATE_DF | Source code |
| .CREATE_DIST_MAT | Source code |
| .CREATE_GRAPH | Source code |
| .DELETE_MULTIPLE_PARENTS | Source code |
| .EDGES | Source code |
| .FIND_EDGES_v1 | Source code |
| .FIND_MATCHES | Source code |
| .FIND_MIN | Source code |
| .GENERATE.BARCODE | Source code |
| .GENERATE.COMBI | Source code |
| .GENERATE_COMBINATIONS | Source code |
| .GRAPH_STRENGTH_DISTRIBUTION | Source code |
| .HAS_EMPTY_LIST | Source code |
| .ISOTYPE_ENCODING | Source code |
| .ISOTYPE_POSITION | Source code |
| .ISOTYPE_TRANSITIONS | Source code |
| .IS_CONTAINED | Source code |
| .LIST_TO_DF | Source code |
| .LONGEST_PATH_FROM_GERMLINE | Source code |
| .MAIN | Source code |
| .MODIFY_INPUT | Source code |
| .NET_TO_COLON_FORMAT | Source code |
| .NODE_DEGREE_EDGES_FROM_GERM | Source code |
| .NODE_DEGREE_PATH_FROM_GERM | Source code |
| .PREPROCESSING | Source code |
| .REFERENCE_INFO | Source code |
| .REMOVE_DUPLICATES | Source code |
| .RM.EMPTY.NODE | Source code |
| .SHM_FUNCTION_SEQUENCE4 | Source code |
| .SPLITCOMBINATION | Source code |
| .SPLITLINEAGES | Source code |
| .TRANS.SWITCH | Source code |
| .TRANS.SWITCH.DEPENDANT | Source code |
| .VDJ_RECOMBIN_FUNCTION | Source code |
| .VERTEX_SCALE | Source code |
| .WRITE.CONSENSUS | Source code |
| .WRITE_TO_PDF | Source code |
| .onehot_encoding | Source code |
| AbForests_AntibodyForest | Man page Source code |
| AbForests_CompareForests | Man page Source code |
| AbForests_ConvertStructure | Man page Source code |
| AbForests_CsvToDf | Man page Source code |
| AbForests_ForestMetrics | Man page Source code |
| AbForests_PlotGraphs | Man page Source code |
| AbForests_PlyloToMatrix | Man page Source code |
| AbForests_RemoveNets | Man page Source code |
| AbForests_SubRepertoiresByCells | Man page Source code |
| AbForests_SubRepertoiresByUniqueSeq | Man page Source code |
| AbForests_UniqueAntibodyVariants | Man page Source code |
| AlphaFold_prediction | Man page Source code |
| AntibodyForests | Man page Source code |
| AntibodyForests_communities | Man page Source code |
| AntibodyForests_dynamics | Man page Source code |
| AntibodyForests_embeddings | Man page Source code |
| AntibodyForests_expand_intermediates | Man page Source code |
| AntibodyForests_heterogeneous | Man page Source code |
| AntibodyForests_infer_ancestral | Man page Source code |
| AntibodyForests_join_trees | Man page Source code |
| AntibodyForests_kernels | Man page Source code |
| AntibodyForests_label_propagation | Man page Source code |
| AntibodyForests_metrics | Man page Source code |
| AntibodyForests_node_transitions | Man page Source code |
| AntibodyForests_overlap | Man page Source code |
| AntibodyForests_paths | Man page Source code |
| AntibodyForests_phylo | Man page Source code |
| AntibodyForests_plot | Man page Source code |
| AntibodyForests_plot_metrics | Man page Source code |
| Bcell_sequences_example_tree | Man page |
| Bcell_tree_2 | Man page |
| CellPhoneDB_analyse | Man page Source code |
| Echidna_simulate_repertoire | Man page Source code |
| Echidna_vae_generate | Man page Source code |
| GEX_DEgenes | Man page Source code |
| GEX_DEgenes_persample | Man page Source code |
| GEX_GOterm | Man page Source code |
| GEX_GSEA | Man page Source code |
| GEX_clonotype | Man page Source code |
| GEX_cluster_genes | Man page Source code |
| GEX_cluster_genes_heatmap | Man page Source code |
| GEX_cluster_membership | Man page Source code |
| GEX_coexpression_coefficient | Man page Source code |
| GEX_dottile_plot | Man page Source code |
| GEX_gene_visualization | Man page Source code |
| GEX_heatmap | Man page Source code |
| GEX_lineage_trajectories | Man page Source code |
| GEX_pairwise_DEGs | Man page Source code |
| GEX_phenotype | Man page Source code |
| GEX_phenotype_per_clone | Man page Source code |
| GEX_projecTILS | Man page Source code |
| GEX_proportions_barplot | Man page Source code |
| GEX_pseudobulk | Man page Source code |
| GEX_pseudotime_trajectory_plot | Man page Source code |
| GEX_scatter_coexpression | Man page Source code |
| GEX_topN_DE_genes_per_cluster | Man page Source code |
| GEX_trajectories | Man page Source code |
| GEX_visualize_clones | Man page Source code |
| GEX_volcano | Man page Source code |
| PlatypusDB_AIRR_to_VGM | Man page Source code |
| PlatypusDB_VGM_to_AIRR | Man page Source code |
| PlatypusDB_fetch | Man page Source code |
| PlatypusDB_find_CDR3s | Man page Source code |
| PlatypusDB_list_projects | Man page Source code |
| PlatypusDB_load_from_disk | Man page Source code |
| PlatypusML_balance | Man page Source code |
| PlatypusML_classification | Man page Source code |
| PlatypusML_feature_extraction_GEX | Man page Source code |
| PlatypusML_feature_extraction_VDJ | Man page Source code |
| Spatial_VDJ_assignment | Man page Source code |
| Spatial_VDJ_plot | Man page Source code |
| Spatial_celltype_plot | Man page Source code |
| Spatial_cluster | Man page Source code |
| Spatial_density_plot | Man page Source code |
| Spatial_evolution_of_clonotype_plot | Man page Source code |
| Spatial_marker_expression | Man page Source code |
| Spatial_module_expression | Man page Source code |
| Spatial_nb_SHM_compare_to_germline_plot | Man page Source code |
| Spatial_scaling_parameters | Man page Source code |
| Spatial_selection_expanded_clonotypes | Man page Source code |
| Spatial_selection_of_cells_on_image | Man page Source code |
| Spatial_vgm_formation | Man page Source code |
| VDJ_GEX_clonal_lineage_clusters | Man page Source code |
| VDJ_GEX_clonotyme | Man page Source code |
| VDJ_GEX_clonotype_clusters_circos | Man page Source code |
| VDJ_GEX_expansion | Man page Source code |
| VDJ_GEX_integrate | Man page Source code |
| VDJ_GEX_matrix | Man page Source code |
| VDJ_GEX_overlay_clones | Man page Source code |
| VDJ_GEX_stats | Man page Source code |
| VDJ_VJ_usage_circos | Man page Source code |
| VDJ_Vgene_usage | Man page Source code |
| VDJ_Vgene_usage_barplot | Man page Source code |
| VDJ_Vgene_usage_stacked_barplot | Man page Source code |
| VDJ_abundances | Man page Source code |
| VDJ_alpha_beta_Vgene_circos | Man page Source code |
| VDJ_analyze | Man page Source code |
| VDJ_antigen_integrate | Man page Source code |
| VDJ_assemble_for_PnP | Man page Source code |
| VDJ_bulk_to_vgm | Man page Source code |
| VDJ_call_MIXCR | Man page Source code |
| VDJ_call_MIXCR_full | Man page |
| VDJ_call_RECON | Man page Source code |
| VDJ_call_enclone | Man page Source code |
| VDJ_circos | Man page Source code |
| VDJ_clonal_donut | Man page Source code |
| VDJ_clonal_expansion | Man page Source code |
| VDJ_clonal_expansion_abundances | Man page Source code |
| VDJ_clonal_lineages | Man page Source code |
| VDJ_clonotype | Man page Source code |
| VDJ_contigs_to_vgm | Man page Source code |
| VDJ_db_annotate | Man page Source code |
| VDJ_db_load | Man page Source code |
| VDJ_diversity | Man page Source code |
| VDJ_dublets | Man page Source code |
| VDJ_dynamics | Man page Source code |
| VDJ_enclone | Man page Source code |
| VDJ_expand_aberrants | Man page Source code |
| VDJ_extract_germline | Man page Source code |
| VDJ_get_public | Man page Source code |
| VDJ_isotypes_per_clone | Man page Source code |
| VDJ_kmers | Man page Source code |
| VDJ_logoplot_vector | Man page Source code |
| VDJ_network | Man page Source code |
| VDJ_ordination | Man page Source code |
| VDJ_overlap_heatmap | Man page Source code |
| VDJ_per_clone | Man page Source code |
| VDJ_phylogenetic_trees | Man page Source code |
| VDJ_phylogenetic_trees_plot | Man page Source code |
| VDJ_plot_SHM | Man page Source code |
| VDJ_public | Man page Source code |
| VDJ_rarefaction | Man page Source code |
| VDJ_reclonotype_list_arrange | Man page Source code |
| VDJ_select_clonotypes | Man page Source code |
| VDJ_structure_analysis | Man page Source code |
| VDJ_tree | Man page Source code |
| VDJ_variants_per_clone | Man page Source code |
| VGM_expand_featurebarcodes | Man page Source code |
| VGM_expanded_clones | Man page Source code |
| VGM_integrate | Man page Source code |
| automate_GEX | Man page Source code |
| call_MIXCR | Man page Source code |
| class_switch_prob_hum | Man page |
| class_switch_prob_mus | Man page |
| clonofreq | Man page Source code |
| clonofreq.isotype.data | Man page Source code |
| clonofreq.isotype.plot | Man page Source code |
| clonofreq.trans.data | Man page Source code |
| clonofreq.trans.plot | Man page Source code |
| cluster.id.igraph | Man page Source code |
| colors | Man page |
| dot_plot | Man page Source code |
| get.avr.mut.data | Man page Source code |
| get.avr.mut.plot | Man page Source code |
| get.barplot.errorbar | Man page Source code |
| get.elbow | Man page Source code |
| get.n.node.data | Man page Source code |
| get.n.node.plot | Man page Source code |
| get.seq.distance | Man page Source code |
| get.umap | Man page Source code |
| get.vgu.matrix | Man page Source code |
| hotspot_df | Man page |
| hum_b_h | Man page |
| hum_b_l | Man page |
| hum_t_h | Man page |
| hum_t_l | Man page |
| iso_SHM_prob | Man page |
| mus_b_h | Man page |
| mus_b_l | Man page |
| mus_b_trans | Man page |
| mus_t_h | Man page |
| mus_t_l | Man page |
| no.empty.node | Man page Source code |
| one_spot_df | Man page |
| pheno_SHM_prob | Man page |
| select.top.clone | Man page Source code |
| small_vgm | Man page |
| special_v | Man page |
| trans_switch_prob_b | Man page |
| trans_switch_prob_t | Man page |
| umap.top.highlight | Man page Source code |
| vdj_length_prob | Man page |
