# Generated by roxygen2: do not edit by hand

export(AbForests_AntibodyForest)
export(AbForests_CompareForests)
export(AbForests_ConvertStructure)
export(AbForests_CsvToDf)
export(AbForests_ForestMetrics)
export(AbForests_PlotGraphs)
export(AbForests_PlyloToMatrix)
export(AbForests_RemoveNets)
export(AbForests_SubRepertoiresByCells)
export(AbForests_SubRepertoiresByUniqueSeq)
export(AbForests_UniqueAntibodyVariants)
export(AlphaFold_prediction)
export(AntibodyForests)
export(AntibodyForests_communities)
export(AntibodyForests_dynamics)
export(AntibodyForests_embeddings)
export(AntibodyForests_heterogeneous)
export(AntibodyForests_infer_ancestral)
export(AntibodyForests_join_trees)
export(AntibodyForests_kernels)
export(AntibodyForests_label_propagation)
export(AntibodyForests_node_transitions)
export(AntibodyForests_overlap)
export(AntibodyForests_paths)
export(AntibodyForests_phylo)
export(AntibodyForests_plot)
export(AntibodyForests_plot_metrics)
export(CellPhoneDB_analyse)
export(Echidna_simulate_repertoire)
export(Echidna_vae_generate)
export(GEX_DEgenes)
export(GEX_DEgenes_persample)
export(GEX_GOterm)
export(GEX_GSEA)
export(GEX_clonotype)
export(GEX_cluster_genes)
export(GEX_cluster_genes_heatmap)
export(GEX_cluster_membership)
export(GEX_coexpression_coefficient)
export(GEX_dottile_plot)
export(GEX_gene_visualization)
export(GEX_heatmap)
export(GEX_lineage_trajectories)
export(GEX_pairwise_DEGs)
export(GEX_phenotype)
export(GEX_phenotype_per_clone)
export(GEX_projecTILS)
export(GEX_proportions_barplot)
export(GEX_pseudobulk)
export(GEX_pseudotime_trajectory_plot)
export(GEX_scatter_coexpression)
export(GEX_topN_DE_genes_per_cluster)
export(GEX_trajectories)
export(GEX_visualize_clones)
export(GEX_volcano)
export(PlatypusDB_AIRR_to_VGM)
export(PlatypusDB_VGM_to_AIRR)
export(PlatypusDB_fetch)
export(PlatypusDB_find_CDR3s)
export(PlatypusDB_list_projects)
export(PlatypusDB_load_from_disk)
export(PlatypusML_feature_extraction_GEX)
export(PlatypusML_feature_extraction_VDJ)
export(Spatial_VDJ_assignment)
export(Spatial_VDJ_plot)
export(Spatial_celltype_plot)
export(Spatial_cluster)
export(Spatial_density_plot)
export(Spatial_evolution_of_clonotype_plot)
export(Spatial_marker_expression)
export(Spatial_module_expression)
export(Spatial_nb_SHM_compare_to_germline_plot)
export(Spatial_scaling_parameters)
export(Spatial_selection_expanded_clonotypes)
export(Spatial_selection_of_cells_on_image)
export(Spatial_vgm_formation)
export(VDJ_GEX_clonal_lineage_clusters)
export(VDJ_GEX_clonotyme)
export(VDJ_GEX_clonotype_clusters_circos)
export(VDJ_GEX_expansion)
export(VDJ_GEX_integrate)
export(VDJ_GEX_matrix)
export(VDJ_GEX_overlay_clones)
export(VDJ_GEX_stats)
export(VDJ_VJ_usage_circos)
export(VDJ_Vgene_usage)
export(VDJ_Vgene_usage_barplot)
export(VDJ_Vgene_usage_stacked_barplot)
export(VDJ_abundances)
export(VDJ_alpha_beta_Vgene_circos)
export(VDJ_analyze)
export(VDJ_antigen_integrate)
export(VDJ_assemble_for_PnP)
export(VDJ_bulk_to_vgm)
export(VDJ_call_MIXCR)
export(VDJ_call_RECON)
export(VDJ_call_enclone)
export(VDJ_circos)
export(VDJ_clonal_donut)
export(VDJ_clonal_expansion)
export(VDJ_clonal_expansion_abundances)
export(VDJ_clonal_lineages)
export(VDJ_clonotype)
export(VDJ_contigs_to_vgm)
export(VDJ_db_annotate)
export(VDJ_db_load)
export(VDJ_diversity)
export(VDJ_dublets)
export(VDJ_dynamics)
export(VDJ_enclone)
export(VDJ_expand_aberrants)
export(VDJ_extract_germline)
export(VDJ_get_public)
export(VDJ_isotypes_per_clone)
export(VDJ_kmers)
export(VDJ_logoplot_vector)
export(VDJ_network)
export(VDJ_ordination)
export(VDJ_overlap_heatmap)
export(VDJ_per_clone)
export(VDJ_phylogenetic_trees)
export(VDJ_phylogenetic_trees_plot)
export(VDJ_plot_SHM)
export(VDJ_public)
export(VDJ_rarefaction)
export(VDJ_reclonotype_list_arrange)
export(VDJ_select_clonotypes)
export(VDJ_structure_analysis)
export(VDJ_tree)
export(VDJ_variants_per_clone)
export(VGM_expand_featurebarcodes)
export(VGM_expanded_clones)
export(VGM_integrate)
export(automate_GEX)
export(call_MIXCR)
export(clonofreq)
export(clonofreq.isotype.data)
export(clonofreq.isotype.plot)
export(clonofreq.trans.data)
export(clonofreq.trans.plot)
export(cluster.id.igraph)
export(dot_plot)
export(get.avr.mut.data)
export(get.avr.mut.plot)
export(get.barplot.errorbar)
export(get.elbow)
export(get.n.node.data)
export(get.n.node.plot)
export(get.seq.distance)
export(get.umap)
export(get.vgu.matrix)
export(no.empty.node)
export(select.top.clone)
export(umap.top.highlight)
importFrom(dplyr,"%>%")
importFrom(foreach,"%dopar%")
importFrom(ggtree,"%<+%")
