Files in Platypus

Single-Cell Immune Repertoire and Gene Expression Analysis

NEWS.md README.md R/AntibodyForests_communities.R R/VDJ_db_load.R R/VDJ_phylogenetic_trees_plot.R R/GEX_volcano.R R/AntibodyForests_embeddings.R R/VDJ_call_recon.R R/AntibodyForests_metrics.R R/VDJ_circos.R R/AbForests_internal.R R/AbForests_PlotGraphs.R R/VDJ_clonal_expansion.R R/GEX_cluster_membership.R R/VDJ_Vgene_usage_barplot.R R/VDJ_structure_analysis.R R/VDJ_clonal_donut.R R/Echidna_Internal_functions.R R/VDJ_Vgene_usage.R R/GEX_heatmap.R R/VGM_expanded_clones.R R/Spatial_density_plot.R R/VDJ_per_clone.R R/GEX_DEgenes.R R/AntibodyForests_plot.R R/VDJ_clonotype.R R/VDJ_clonal_lineages.R R/VDJ_public.R R/Echidna_other_functions.R R/GEX_cluster_genes.R R/GEX_topN_DE_genes_per_cluster.R R/VDJ_logoplot_vector.R R/VDJ_phylogenetic_trees.R R/VDJ_overlap_heatmap.R R/VDJ_dynamics.R R/GEX_proportions_barplot.R R/Echidna_vae_generate.R R/GEX_projecTILS.R R/Spatial_cluster.R R/AntibodyForests_infer_ancestral.R R/Spatial_marker_expression.R R/VDJ_ordination.R R/Spatial_scaling_parameters.R R/PlatypusML_feature_extraction_VDJ.R R/Spatial_VDJ_plot.R R/PlatypusML_balance.R R/Echidna_data.R R/AbForests_PlyloToMatrix.R R/PlatypusML_classification.R R/VDJ_isotypes_per_clone.R R/VDJ_extract_germline.R R/dot_plot.R R/AntibodyForests_expand_intermediates.R R/VDJ_assemble_for_PnP.R R/VDJ_variants_per_clone.R R/GEX_GSEA.R R/GEX_visualize_clones.R R/AbForests_CsvToDf.R R/Spatial_selection_of_cells_on_image.R R/VDJ_analyze.R R/VDJ_kmers.R R/PlatypusDB_list_projects.R R/VDJ_GEX_matrix.R R/VDJ_GEX_expansion.R R/VDJ_dublets.R R/GEX_phenotype.R R/Spatial_celltype_plot.R R/VDJ_antigen_integrate.R R/AntibodyForests_phylo.R R/PlatypusDB_AIRR_to_VGM.R R/GEX_trajectories.R R/Echidna_simulate_repertoire.R R/VDJ_Vgene_usage_stacked_barplot.R R/AbForests_UniqueAntibodyVariants.R R/PlatypusDB_find_CDR3s.R R/VDJ_call_MIXCR_full.R R/GEX_GOterm.R R/AntibodyForests_join_trees.R R/CellPhoneDB_analyse.R R/VDJ_GEX_clonotype_clusters_circos.R R/VDJ_GEX_clonotyme.R R/AntibodyForests_node_transitions.R R/AntibodyForests_heterogeneous.R R/VDJ_alpha_beta_Vgene_circos.R R/VDJ_GEX_stats.R R/VDJ_call_MIXCR.R R/VDJ_select_clonotypes.R R/VDJ_GEX_overlay_clones.R R/Spatial_evolution_of_clonotype_plot.R R/PlatypusDB_load_from_disk.R R/AntibodyForests_paths.R R/GEX_scatter_coexpression.R R/Spatial_nb_SHM_compare_to_germline_plot.R R/VDJ_VJ_usage_circos.R R/Echidna_vae_internal_functions.R R/PlatypusML_feature_extraction_GEX.R R/GEX_pairwise_degs.R R/AbForests_ForestMetrics.R R/AbForests_SubRepertoiresByUniqueSeq.R R/VDJ_diversity.R R/call_MIXCR.R R/GEX_lineage_trajectories.R R/PlatypusDB_fetch.R R/VDJ_tree.R R/Spatial_vgm_formation.R R/GEX_gene_visualization.R R/GEX_DEgenes_persample.R R/VDJ_bulk_to_vgm.R R/AbForests_RemoveNets.R R/GEX_dottile_plot.R R/AntibodyForests_plot_metrics.R R/AntibodyForests_label_propagation.R R/GEX_clonotype.R R/automate_GEX.R R/AbForests_data.R R/AbForests_CompareForests.R R/Platypus_data.R R/AntibodyForests_overlap.R R/Spatial_VDJ_assignment.R R/VDJ_enclone.R R/GEX_pseudotime_trajectory_plot.R R/VDJ_network.R R/GEX_cluster_genes_heatmap.R R/VDJ_abundances.R R/VDJ_reclonotype_list_arrange.R R/AbForests_SubRepertoiresByCells.R R/VDJ_expand_aberrants.R R/VDJ_rarefaction.R R/VGM_integrate.R R/VDJ_db_annotate.R R/VDJ_GEX_clonal_lineage_clusters.R R/AntibodyForests_kernels.R R/VDJ_contigs_to_vgm.R R/VDJ_call_enclone.R R/Spatial_module_expression.R R/GEX_phenotype_per_clone.R R/PlatypusDB_VGM_to_AIRR.R R/Spatial_selection_expanded_clonotypes.R R/AntibodyForests_dynamics.R R/AlphaFold_prediction.R R/AbForests_AntibodyForest.R R/VGM_expand_featurebarcodes.R R/VDJ_plot_SHM.R R/GEX_coexpression_coefficient.R R/AbForests_ConvertStructure.R R/VDJ_clonal_expansion_abundances.R R/GEX_pseudobulk.R R/VDJ_GEX_integrate.R R/AntibodyForests.R R/VDJ_get_public.R inst/doc/PlatypusV3_agedCNS.Rmd inst/doc/PlatypusV3_agedCNS.R vignettes/PlatypusV3_agedCNS.Rmd vignettes/out/subsampled/plot.pdf vignettes/out/subsampled/heatmap_log_count.pdf vignettes/out/subsampled/selection_plot.pdf vignettes/out/subsampled/heatmap_count.pdf man/AbForests_CsvToDf.Rd man/GEX_GSEA.Rd man/select.top.clone.Rd man/AbForests_UniqueAntibodyVariants.Rd man/hum_t_l.Rd man/Spatial_marker_expression.Rd man/VDJ_reclonotype_list_arrange.Rd man/Spatial_cluster.Rd man/AntibodyForests_communities.Rd man/clonofreq.Rd man/Spatial_evolution_of_clonotype_plot.Rd man/mus_b_l.Rd man/VDJ_VJ_usage_circos.Rd man/Spatial_module_expression.Rd man/VDJ_call_enclone.Rd man/GEX_projecTILS.Rd man/GEX_DEgenes_persample.Rd man/VDJ_phylogenetic_trees_plot.Rd man/PlatypusML_balance.Rd man/automate_GEX.Rd man/AntibodyForests_label_propagation.Rd man/Echidna_simulate_repertoire.Rd man/vdj_length_prob.Rd man/GEX_cluster_genes.Rd man/VDJ_contigs_to_vgm.Rd man/clonofreq.trans.data.Rd man/GEX_GOterm.Rd man/AntibodyForests_expand_intermediates.Rd man/VDJ_clonotype.Rd man/VGM_expanded_clones.Rd man/Spatial_density_plot.Rd man/VDJ_GEX_stats.Rd man/VDJ_rarefaction.Rd man/PlatypusML_feature_extraction_VDJ.Rd man/Spatial_VDJ_plot.Rd man/AntibodyForests.Rd man/VDJ_structure_analysis.Rd man/VDJ_clonal_expansion_abundances.Rd man/mus_b_h.Rd man/AntibodyForests_phylo.Rd man/AbForests_AntibodyForest.Rd man/AbForests_CompareForests.Rd man/GEX_lineage_trajectories.Rd man/VDJ_select_clonotypes.Rd man/small_vgm.Rd man/Spatial_celltype_plot.Rd man/iso_SHM_prob.Rd man/AntibodyForests_paths.Rd man/umap.top.highlight.Rd man/VDJ_GEX_clonotype_clusters_circos.Rd man/GEX_pairwise_DEGs.Rd man/no.empty.node.Rd man/VDJ_GEX_clonal_lineage_clusters.Rd man/hum_t_h.Rd man/AbForests_ConvertStructure.Rd man/trans_switch_prob_t.Rd man/VDJ_clonal_donut.Rd man/AbForests_SubRepertoiresByUniqueSeq.Rd man/get.vgu.matrix.Rd man/PlatypusDB_find_CDR3s.Rd man/Spatial_selection_expanded_clonotypes.Rd man/PlatypusDB_list_projects.Rd man/hotspot_df.Rd man/PlatypusDB_load_from_disk.Rd man/VDJ_per_clone.Rd man/VDJ_GEX_integrate.Rd man/clonofreq.isotype.data.Rd man/get.avr.mut.data.Rd man/VDJ_GEX_matrix.Rd man/get.avr.mut.plot.Rd man/VDJ_GEX_clonotyme.Rd man/Bcell_sequences_example_tree.Rd man/VDJ_abundances.Rd man/VDJ_call_MIXCR.Rd man/GEX_cluster_genes_heatmap.Rd man/VDJ_call_MIXCR_full.Rd man/Spatial_nb_SHM_compare_to_germline_plot.Rd man/AbForests_ForestMetrics.Rd man/GEX_heatmap.Rd man/AntibodyForests_plot_metrics.Rd man/GEX_pseudobulk.Rd man/get.n.node.data.Rd man/VDJ_logoplot_vector.Rd man/CellPhoneDB_analyse.Rd man/clonofreq.trans.plot.Rd man/clonofreq.isotype.plot.Rd man/AntibodyForests_join_trees.Rd man/Spatial_vgm_formation.Rd man/GEX_gene_visualization.Rd man/VDJ_expand_aberrants.Rd man/VDJ_alpha_beta_Vgene_circos.Rd man/VDJ_clonal_expansion.Rd man/GEX_trajectories.Rd man/VDJ_dynamics.Rd man/VDJ_public.Rd man/PlatypusML_classification.Rd man/AntibodyForests_node_transitions.Rd man/VDJ_clonal_lineages.Rd man/VDJ_enclone.Rd man/VDJ_analyze.Rd man/AntibodyForests_embeddings.Rd man/call_MIXCR.Rd man/VDJ_bulk_to_vgm.Rd man/GEX_proportions_barplot.Rd man/hum_b_l.Rd man/VDJ_variants_per_clone.Rd man/VDJ_ordination.Rd man/VDJ_assemble_for_PnP.Rd man/PlatypusDB_VGM_to_AIRR.Rd man/class_switch_prob_mus.Rd man/hum_b_h.Rd man/mus_t_l.Rd man/VDJ_dublets.Rd man/VDJ_plot_SHM.Rd man/pheno_SHM_prob.Rd man/VDJ_phylogenetic_trees.Rd man/AntibodyForests_overlap.Rd man/GEX_visualize_clones.Rd man/get.elbow.Rd man/GEX_dottile_plot.Rd man/special_v.Rd man/VDJ_diversity.Rd man/VDJ_network.Rd man/get.n.node.plot.Rd man/GEX_coexpression_coefficient.Rd man/VGM_integrate.Rd man/Spatial_selection_of_cells_on_image.Rd man/GEX_pseudotime_trajectory_plot.Rd man/mus_b_trans.Rd man/GEX_phenotype.Rd man/AbForests_RemoveNets.Rd man/AntibodyForests_metrics.Rd man/GEX_scatter_coexpression.Rd man/GEX_phenotype_per_clone.Rd man/VDJ_GEX_expansion.Rd man/VDJ_kmers.Rd man/Echidna_vae_generate.Rd man/VDJ_antigen_integrate.Rd man/Spatial_scaling_parameters.Rd man/VDJ_overlap_heatmap.Rd man/class_switch_prob_hum.Rd man/one_spot_df.Rd man/get.barplot.errorbar.Rd man/AntibodyForests_plot.Rd man/GEX_volcano.Rd man/get.seq.distance.Rd man/VDJ_Vgene_usage_barplot.Rd man/AntibodyForests_dynamics.Rd man/GEX_clonotype.Rd man/VDJ_Vgene_usage.Rd man/VDJ_circos.Rd man/AntibodyForests_heterogeneous.Rd man/AbForests_SubRepertoiresByCells.Rd man/VDJ_get_public.Rd man/VDJ_db_annotate.Rd man/AbForests_PlotGraphs.Rd man/VDJ_GEX_overlay_clones.Rd man/VGM_expand_featurebarcodes.Rd man/GEX_DEgenes.Rd man/trans_switch_prob_b.Rd man/cluster.id.igraph.Rd man/AlphaFold_prediction.Rd man/GEX_cluster_membership.Rd man/colors.Rd man/dot_plot.Rd man/VDJ_db_load.Rd man/Spatial_VDJ_assignment.Rd man/PlatypusDB_AIRR_to_VGM.Rd man/Bcell_tree_2.Rd man/VDJ_call_RECON.Rd man/AntibodyForests_infer_ancestral.Rd man/AbForests_PlyloToMatrix.Rd man/VDJ_tree.Rd man/PlatypusML_feature_extraction_GEX.Rd man/get.umap.Rd man/VDJ_isotypes_per_clone.Rd man/mus_t_h.Rd man/GEX_topN_DE_genes_per_cluster.Rd man/PlatypusDB_fetch.Rd man/AntibodyForests_kernels.Rd man/VDJ_Vgene_usage_stacked_barplot.Rd man/VDJ_extract_germline.Rd