Single-Cell Immune Repertoire and Gene Expression Analysis

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Documentation for package ‘Platypus’ version 3.5.0

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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_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. Optimized for for Cell Ranger v7 and suitable for older Cell Ranger versions.
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_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