Man pages for Platypus
Single-Cell Immune Repertoire and Gene Expression Analysis

GEX_cluster_genesDifferentially expressed genes between clusters or data...
GEX_cluster_genes_heatmapHeatmap of cluster defining genes
GEX_cluster_membershipCluster membership plots by sample
GEX_coexpression_coefficientCoexpression of selected genes
GEX_DEgenesWrapper for differential gene expression analysis and...
GEX_dottile_plotGEX Dottile plots
GEX_gene_visualizationVisualization of marker expression in a data set or of...
GEX_GSEAGEX Gene Set Enrichment Analysis and plotting
GEX_heatmapFlexible GEX heatmap wrapper
GEX_lineage_trajectoriesThis is a function to infer single cell trajectories and...
GEX_pairwise_DEGsWrapper for calculating pairwise differentially expressed...
GEX_phenotypeAssignment of cells to phenotypes based on selected markers
GEX_phenotype_per_clonePlotting of GEX phenotype by VDJ clone
GEX_proportions_barplotPlots proportions of a group of cells within a secondary...
GEX_scatter_coexpressionScatter plot for coexpression of two selected genes
GEX_volcanoFlexible wrapper for GEX volcano plots
PlatypusDB_AIRR_to_VGMAIRR to Platypus V3 VGM compatibility function
PlatypusDB_load_from_diskPlatypusDB utility for import of local datasets
PlatypusDB_VGM_to_AIRRPlatypus V3 VGM to AIRR compatibility function
small_vdjSmall VDJ dataframe for function testing purposes
small_vgmSmall VDJ GEX matrix (VGM) for function testing purposes
VDJ_abundancesCalculate abundances/counts of specific features for a VDJ...
VDJ_alpha_beta_Vgene_circosProduces a Circos plot from the VDJ_analyze output. Connects...
VDJ_antigen_integrateIntegrates antigen-specific information into the...
VDJ_assemble_for_PnPAb sequence assembly for recombinant PnP expression
VDJ_buildMinimal Version of the VDJ Building Part from...
VDJ_call_enclone(Re)clonotype a VDJ object using cellranger's enclone tool
VDJ_circosPlots a Circos diagram from an adjacency matrix. Uses the...
VDJ_clonal_barplotFunction to create stacked barplots to visualize clonal...
VDJ_clonal_donutCircular VDJ expansion plots
VDJ_clonal_expansionFlexible wrapper for clonal expansion barplots by isotype,...
VDJ_clonotypePlatypus V3 clonotyping wrapper
VDJ_clonotype_v3_w_encloneUpdated clonotyping function based on implications for cells...
VDJ_contigs_to_vgmFormats "VDJ_contigs_annotations.csv" files from cell ranger...
VDJ_db_annotateWrapper function of VDJ_antigen_integrate function
VDJ_db_loadLoad and preprocess a list of antigen-specific databases
VDJ_diversityCalculates and plots common diversity and overlap measures...
VDJ_dynamicsTracks a specific VDJ column across multiple...
VDJ_expand_aberrantsExpand the aberrant cells in a VDJ dataframe by converting...
VDJ_extract_germline_consensus_refMaking the trimmed reference and concatenating fr1-fr4
VDJ_germlineInfer germline from the desired software/caller
VDJ_get_publicFunction to get shared/public elements across multiple...
VDJ_GEX_clonotype_clusters_circosMakes a Circos plot from the VDJ_GEX_integrate output....
VDJ_GEX_matrixVDJ GEX processing and integration wrapper
VDJ_GEX_overlay_clonesOverlay clones on GEX projection
VDJ_GEX_statsStandalone VDJ and GEX statistics.
VDJ_kmersCalculates and plots kmers distributions and frequencies.
VDJ_logoplot_vectorFlexible logoplot wrapper
VDJ_networkSimilarity networks based on CDR3 regions
VDJ_ordinationPerforms ordination/dimensionality reduction for a species...
VDJ_overlap_heatmapWrapper to determine and plot overlap between VDJ features...
VDJ_phylogenetic_treesCreates phylogenetic trees from a VDJ dataframe
VDJ_phylogenetic_trees_plotPhylogenetic tree plotting
VDJ_plot_SHMPlotting of somatic hypermutation counts
VDJ_publicFunction to get shared/public elements across multiple...
VDJ_rarefactionPlots rarefaction curves for species denoted in the...
VDJ_variants_per_cloneWrapper for variant analysis by clone
VDJ_Vgene_usageV(D)J gene usage stacked barplots
VDJ_Vgene_usage_barplotV(D)J gene usage barplots
VDJ_Vgene_usage_stacked_barplotV(D)J gene usage stacked barplots
VDJ_VJ_usage_circosMakes a Circos plot from the VDJ_analyze output. Connects the...
VGM_buildFunction to obtain the VGM object by integrating the VDJ and...
VGM_expanded_clonesVDJ utility for T/F column for clonal expansion
VGM_expand_featurebarcodesUtility for feature barcode assignment including clonal...
VGM_integrateUtility for VDJ GEX matrix to integrated VDJ and GEX objects...
Platypus documentation built on Oct. 18, 2024, 5:08 p.m.