Man pages for Platypus
Single-Cell Immune Repertoire and Gene Expression Analysis
| AbForests_AntibodyForest | Infer and draw B cell evolutionary networks |
| AbForests_CompareForests | Comparison of distinct B cell repertoires |
| AbForests_ConvertStructure | Extract transcriptome/isotype information and B cell receptor... |
| AbForests_CsvToDf | Convert list of csvs, to nested list of data.frames |
| AbForests_ForestMetrics | Calculate metrics for networks |
| AbForests_PlotGraphs | Plot igraph and ggplot objects |
| AbForests_PlyloToMatrix | Conversion of phylogenetic tree to distance matrix |
| AbForests_RemoveNets | Filter sub-repertoires with less than N unique sequences or... |
| AbForests_SubRepertoiresByCells | Split single cell immune repertoire into sub-repertoires by... |
| AbForests_SubRepertoiresByUniqueSeq | Split single cell immune repertoire into sub-repertoires by... |
| AbForests_UniqueAntibodyVariants | Count the number of unique antibody variants per clonal... |
| AlphaFold_prediction | Structure prediction of Mixcr wrapper output with Alpha Fold |
| AntibodyForests | Infer B cell evolutionary networks and/or sequence similarity... |
| AntibodyForests_communities | Network clustering/community detection for the... |
| AntibodyForests_dynamics | Create a nested list of longitudinal AntibodyForests objects |
| AntibodyForests_embeddings | Structural node embeddings for the AntibodyForests minimum... |
| AntibodyForests_expand_intermediates | Infer intermediate nodes in the minimum spanning trees/... |
| AntibodyForests_heterogeneous | Bipartite sequence-cell networks in AntibodyForests |
| AntibodyForests_infer_ancestral | Creates phylogenetic trees, infers ancestral sequences, and... |
| AntibodyForests_join_trees | Joins a list of trees/networks as AntibodyForests objects... |
| AntibodyForests_kernels | Graph kernel methods for graph structure/topology comparisons |
| AntibodyForests_label_propagation | Propagate label annotations/values on sparsely labeled... |
| AntibodyForests_metrics | Node metrics for the AntibodyForests sequence similarity... |
| AntibodyForests_node_transitions | Calculates the node transitions frequencies for a given... |
| AntibodyForests_overlap | Edge overlap heatmaps for a set of AntibodyForests sequence... |
| AntibodyForests_paths | Calculates the longest/shortest paths from a node to a given... |
| AntibodyForests_phylo | Converts the igraph networks of a given AntibodyForests... |
| AntibodyForests_plot | Custom plots for trees/networks created with AntibodyForests |
| AntibodyForests_plot_metrics | Plots the resulting node metrics from the... |
| automate_GEX | GEX processing wrapper in Platypus V2 |
| Bcell_sequences_example_tree | Example csv file 1 |
| Bcell_tree_2 | Example csv file 2 |
| call_MIXCR | Calls MiXCR VDJ object of Platypus V2 |
| CellPhoneDB_analyse | Cellphone DB utility |
| class_switch_prob_hum | class_switch_prob_hum The probability matrix of class... |
| class_switch_prob_mus | class_switch_prob_mus The probability matrix of class... |
| clonofreq | Plot clonal frequency barplot of the outout simulated data |
| clonofreq.isotype.data | Get information about the clonotype counts grouped by... |
| clonofreq.isotype.plot | Get information about the clonotype counts grouped by... |
| clonofreq.trans.data | Get information about the clonotype counts grouped by... |
| clonofreq.trans.plot | Get information about the clonotype counts grouped by... |
| cluster.id.igraph | Get clone network igraphs colored by seurat cluster id. |
| colors | colors A vector of characters specifying colors used in... |
| dot_plot | Function to cutomise the Dot Plot of CellPhoneDB analysis... |
| Echidna_simulate_repertoire | Simulate immune repertoire and transcriptome data |
| Echidna_vae_generate | Simulate B or T cell receptor sequences by variational... |
| get.avr.mut.data | Get information about somatic hypermutation in the... |
| get.avr.mut.plot | Get information about somatic hypermutation in the... |
| get.barplot.errorbar | Return a barplot of mean and standard error bar of certain... |
| get.elbow | Get the seurat object from simulated transciptome output. |
| get.n.node.data | Get the number of unique variants in each clone in a vector.... |
| get.n.node.plot | Get the number of unique variants in each clone in a vector... |
| get.seq.distance | Computing sequence distance according to the number of... |
| get.umap | Further process the seurat object from simulated transciptome... |
| get.vgu.matrix | Get paired v gene heavy chain and light chain matrix on... |
| GEX_clonotype | Platypus V2 GEX and VDJ integration for clonotypes |
| 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_DEgenes_persample | Platypus V2 Differentially expressed genes |
| GEX_dottile_plot | GEX Dottile plots |
| GEX_gene_visualization | Visualization of marker expression in a data set or of... |
| GEX_GOterm | GEX GO-Term analysis and plotting |
| 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_projecTILS | ProjectTILs tool utility |
| GEX_proportions_barplot | Plots proportions of a group of cells within a secondary... |
| GEX_pseudobulk | Function that performs pseudo-bulking on the data (VGM... |
| GEX_pseudotime_trajectory_plot | This function plots pseudotime along the trajectories which... |
| GEX_scatter_coexpression | Scatter plot for coexpression of two selected genes |
| GEX_topN_DE_genes_per_cluster | Platypus V2 GEX DE genes helper |
| GEX_trajectories | This is a function which infers trajectories along ordered... |
| GEX_visualize_clones | Platypus V2 GEX and VDJ integration for visualizing clone... |
| GEX_volcano | Flexible wrapper for GEX volcano plots |
| hotspot_df | hotspot_df Hotspot mutations taken from Yaari et al.,... |
| hum_b_h | hum_b_h |
| hum_b_l | hum_b_l |
| hum_t_h | hum_t_h |
| hum_t_l | hum_t_l |
| iso_SHM_prob | iso_SHM_prob A probability dataframe specifying SHM.nuc.prob... |
| mus_b_h | mus_b_h |
| mus_b_l | mus_b_l |
| mus_b_trans | mus_b_trans A data frame contains mouse B cell average gene... |
| mus_t_h | mus_t_h |
| mus_t_l | mus_t_l |
| no.empty.node | Get clone network igraphs without empty mode. Empty node... |
| one_spot_df | one_spot_df |
| pheno_SHM_prob | pheno_SHM_prob A probability dataframe specifying... |
| PlatypusDB_AIRR_to_VGM | AIRR to Platypus V3 VGM compatibility function |
| PlatypusDB_fetch | Loads and saves RData objects from the PlatypusDB |
| PlatypusDB_find_CDR3s | CDR3 query function for PlatypusDB |
| PlatypusDB_list_projects | Metadata download by project for PlatypusDB |
| PlatypusDB_load_from_disk | PlatypusDB utility for import of local datasets |
| PlatypusDB_VGM_to_AIRR | Platypus V3 VGM to AIRR compatibility function |
| PlatypusML_balance | Secondary ML for crossvalidation |
| PlatypusML_classification | Core ML for crossvalidation |
| PlatypusML_feature_extraction_GEX | Extraction of features from GEX matrix of VGM |
| PlatypusML_feature_extraction_VDJ | Extraction of features from VDJ table of VGM |
| select.top.clone | Get the index of top ranking clones. |
| small_vgm | Small VDJ GEX matrix (VGM) for function testing purposes |
| Spatial_celltype_plot | Plotting celltype assign to cell according to their phenotype... |
| Spatial_cluster | Plotting clusters of cells by choosing between 10X Genomics... |
| Spatial_density_plot | Plotting the contour density of selected cells or of all... |
| Spatial_evolution_of_clonotype_plot | Plotting the phylogenetic network of a clonotype based on the... |
| Spatial_marker_expression | Plotting a gene of interest in selected cells on the spatial... |
| Spatial_module_expression | Plotting the expression of a gene module on the spatial image... |
| Spatial_nb_SHM_compare_to_germline_plot | Plotting number of somatic hypermutation of clones compare to... |
| Spatial_scaling_parameters | Scaling of the spatial parameters to be able to express the... |
| Spatial_selection_expanded_clonotypes | Selection of VGM[[1]]/VDJ data of the x more expanded... |
| Spatial_selection_of_cells_on_image | Allows to select an area on the spatial image and to isolate... |
| Spatial_VDJ_assignment | Assign simulated immune repertoire sequences (BCR or TCR)... |
| Spatial_VDJ_plot | Plotting immune repertoire data as clonotype or isotype for... |
| Spatial_vgm_formation | Addition of the spatial information to the VGM matrix, output... |
| special_v | special_v a dataframe, of heavy and light chain v gene... |
| trans_switch_prob_b | trans_switch_prob_b The probability for B cell transcriptome... |
| trans_switch_prob_t | trans_switch_prob_t The probability for T cell transcriptome... |
| umap.top.highlight | Set idents for top abundant clones in Seurat object, get... |
| 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_analyze | Platypus V2 VDJ processing wrapper. |
| VDJ_antigen_integrate | Integrates antigen-specific information into the... |
| VDJ_assemble_for_PnP | Ab sequence assembly for recombinant PnP expression |
| VDJ_bulk_to_vgm | Utility function for bulk data to standard Platypus format... |
| VDJ_call_enclone | (Re)clonotype a VDJ object using cellranger's enclone tool |
| VDJ_call_MIXCR | MiXCR wrapper for Platypus V3 VDJ object |
| VDJ_call_MIXCR_full | MiXCR wrapper for Platypus V3 VDJ object. In addition to the... |
| VDJ_call_RECON | Calls the Kaplinsky/RECON tool |
| VDJ_circos | Plots a Circos diagram from an adjacency matrix. Uses the... |
| VDJ_clonal_donut | Circular VDJ expansion plots |
| VDJ_clonal_expansion | Flexible wrapper for clonal expansion barplots by isotype,... |
| VDJ_clonal_expansion_abundances | Wrapper function for VDJ_abundances to obtain ranked... |
| VDJ_clonal_lineages | Platypus V2 lineage utility |
| VDJ_clonotype | Platypus V3 clonotyping wrapper |
| 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_dublets | Platypus V2 annotation utility |
| VDJ_dynamics | Tracks a specific VDJ column across multiple... |
| VDJ_enclone | Updated clonotyping function based on implications for cells... |
| VDJ_expand_aberrants | Expand the aberrant cells in a VDJ dataframe by converting... |
| VDJ_extract_germline | Platypus V2 utility for full germline sequence via MiXCR |
| VDJ_get_public | Function to get shared/public elements across multiple... |
| VDJ_GEX_clonal_lineage_clusters | Platypus V2 lineage - GEX integration utility |
| VDJ_GEX_clonotyme | Pseudotime analysis for scRNA and repertoire sequencing... |
| VDJ_GEX_clonotype_clusters_circos | Makes a Circos plot from the VDJ_GEX_integrate output.... |
| VDJ_GEX_expansion | Platypus V2 utility |
| VDJ_GEX_integrate | only Platypus v2 Integrates VDJ and gene expression libraries... |
| 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_isotypes_per_clone | Platypus V2 clonal utility |
| VDJ_kmers | Calculates and plots kmers distributions and frequencies. |
| vdj_length_prob | vdj_length_prob A list dataframe specifying lengths and... |
| 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_per_clone | VDJ_per_clone |
| 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_reclonotype_list_arrange | Platypus V2 dataframe utility |
| VDJ_select_clonotypes | Select clonotypes |
| VDJ_structure_analysis | Analysis of antibody structures |
| VDJ_tree | Platypus V2 phylogenetic trees. |
| 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_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... |
