R Packages that start with:
A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .
Functions
- AbForests_AntibodyForest()
- AbForests_CompareForests()
- AbForests_ConvertStructure()
- AbForests_CsvToDf()
- AbForests_ForestMetrics()
- AbForests_PlotGraphs()
- AbForests_PlyloToMatrix()
- AbForests_RemoveNets()
- AbForests_SubRepertoiresByCells()
- AbForests_SubRepertoiresByUniqueSeq()
- AbForests_UniqueAntibodyVariants()
- AlphaFold_prediction()
- AntibodyForests()
- AntibodyForests_communities()
- AntibodyForests_dynamics()
- AntibodyForests_embeddings()
- AntibodyForests_expand_intermediates()
- AntibodyForests_heterogeneous()
- AntibodyForests_infer_ancestral()
- AntibodyForests_join_trees()
- AntibodyForests_kernels()
- AntibodyForests_label_propagation()
- AntibodyForests_metrics()
- AntibodyForests_node_transitions()
- AntibodyForests_overlap()
- AntibodyForests_paths()
- AntibodyForests_phylo()
- AntibodyForests_plot()
- AntibodyForests_plot_metrics()
- automate_GEX()
- Bcell_sequences_example_tree()
- Bcell_tree_2()
- call_MIXCR()
- CellPhoneDB_analyse()
- class_switch_prob_hum()
- class_switch_prob_mus()
- clonofreq.isotype.data()
- clonofreq.isotype.plot()
- clonofreq()
- clonofreq.trans.data()
- clonofreq.trans.plot()
- cluster.id.igraph()
- colors()
- dot_plot()
- Echidna_simulate_repertoire()
- Echidna_vae_generate()
- get.avr.mut.data()
- get.avr.mut.plot()
- get.barplot.errorbar()
- get.elbow()
- get.n.node.data()
- get.n.node.plot()
- get.seq.distance()
- get.umap()
- get.vgu.matrix()
- GEX_clonotype()
- GEX_cluster_genes()
- GEX_cluster_genes_heatmap()
- GEX_cluster_membership()
- GEX_coexpression_coefficient()
- GEX_DEgenes()
- GEX_DEgenes_persample()
- GEX_dottile_plot()
- GEX_gene_visualization()
- GEX_GOterm()
- GEX_GSEA()
- GEX_heatmap()
- GEX_lineage_trajectories()
- GEX_pairwise_DEGs()
- GEX_phenotype()
- GEX_phenotype_per_clone()
- GEX_projecTILS()
- GEX_proportions_barplot()
- GEX_pseudobulk()
- GEX_pseudotime_trajectory_plot()
- GEX_scatter_coexpression()
- GEX_topN_DE_genes_per_cluster()
- GEX_trajectories()
- GEX_visualize_clones()
- GEX_volcano()
- hotspot_df()
- hum_b_h()
- hum_b_l()
- hum_t_h()
- hum_t_l()
- iso_SHM_prob()
- mus_b_h()
- mus_b_l()
- mus_b_trans()
- mus_t_h()
- mus_t_l()
- no.empty.node()
- one_spot_df()
- pheno_SHM_prob()
- PlatypusDB_AIRR_to_VGM()
- PlatypusDB_fetch()
- PlatypusDB_find_CDR3s()
- PlatypusDB_list_projects()
- PlatypusDB_load_from_disk()
- PlatypusDB_VGM_to_AIRR()
- PlatypusML_balance()
- PlatypusML_classification()
- PlatypusML_feature_extraction_GEX()
- PlatypusML_feature_extraction_VDJ()
- select.top.clone()
- small_vgm()
- Spatial_celltype_plot()
- Spatial_cluster()
- Spatial_density_plot()
- Spatial_evolution_of_clonotype_plot()
- Spatial_marker_expression()
- Spatial_module_expression()
- Spatial_nb_SHM_compare_to_germline_plot()
- Spatial_scaling_parameters()
- Spatial_selection_expanded_clonotypes()
- Spatial_selection_of_cells_on_image()
- Spatial_VDJ_assignment()
- Spatial_VDJ_plot()
- Spatial_vgm_formation()
- special_v()
- trans_switch_prob_b()
- trans_switch_prob_t()
- umap.top.highlight()
- VDJ_abundances()
- VDJ_alpha_beta_Vgene_circos()
- VDJ_analyze()
- VDJ_antigen_integrate()
- VDJ_assemble_for_PnP()
- VDJ_bulk_to_vgm()
- VDJ_call_enclone()
- VDJ_call_MIXCR()
- VDJ_call_MIXCR_full()
- VDJ_call_RECON()
- VDJ_circos()
- VDJ_clonal_donut()
- VDJ_clonal_expansion()
- VDJ_clonal_expansion_abundances()
- VDJ_clonal_lineages()
- VDJ_clonotype()
- VDJ_contigs_to_vgm()
- VDJ_db_annotate()
- VDJ_db_load()
- VDJ_diversity()
- VDJ_dublets()
- VDJ_dynamics()
- VDJ_enclone()
- VDJ_expand_aberrants()
- VDJ_extract_germline()
- VDJ_get_public()
- VDJ_GEX_clonal_lineage_clusters()
- VDJ_GEX_clonotyme()
- VDJ_GEX_clonotype_clusters_circos()
- VDJ_GEX_expansion()
- VDJ_GEX_integrate()
- VDJ_GEX_matrix()
- VDJ_GEX_overlay_clones()
- VDJ_GEX_stats()
- VDJ_isotypes_per_clone()
- VDJ_kmers()
- vdj_length_prob()
- VDJ_logoplot_vector()
- VDJ_network()
- VDJ_ordination()
- VDJ_overlap_heatmap()
- VDJ_per_clone()
- VDJ_phylogenetic_trees()
- VDJ_phylogenetic_trees_plot()
- VDJ_plot_SHM()
- VDJ_public()
- VDJ_rarefaction()
- VDJ_reclonotype_list_arrange()
- VDJ_select_clonotypes()
- VDJ_structure_analysis()
- VDJ_tree()
- VDJ_variants_per_clone()
- VDJ_Vgene_usage()
- VDJ_Vgene_usage_barplot()
- VDJ_Vgene_usage_stacked_barplot()
- VDJ_VJ_usage_circos()
- VGM_expanded_clones()
- VGM_expand_featurebarcodes()
- VGM_integrate()
R Codes
- AbForests_AntibodyForest.R
- AbForests_CompareForests.R
- AbForests_ConvertStructure.R
- AbForests_CsvToDf.R
- AbForests_data.R
- AbForests_ForestMetrics.R
- AbForests_internal.R
- AbForests_PlotGraphs.R
- AbForests_PlyloToMatrix.R
- AbForests_RemoveNets.R
- AbForests_SubRepertoiresByCells.R
- AbForests_SubRepertoiresByUniqueSeq.R
- AbForests_UniqueAntibodyVariants.R
- AlphaFold_prediction.R
- AntibodyForests.R
- AntibodyForests_communities.R
- AntibodyForests_dynamics.R
- AntibodyForests_embeddings.R
- AntibodyForests_expand_intermediates.R
- AntibodyForests_heterogeneous.R
- AntibodyForests_infer_ancestral.R
- AntibodyForests_join_trees.R
- AntibodyForests_kernels.R
- AntibodyForests_label_propagation.R
- AntibodyForests_metrics.R
- AntibodyForests_node_transitions.R
- AntibodyForests_overlap.R
- AntibodyForests_paths.R
- AntibodyForests_phylo.R
- AntibodyForests_plot.R
- AntibodyForests_plot_metrics.R
- automate_GEX.R
- call_MIXCR.R
- CellPhoneDB_analyse.R
- dot_plot.R
- Echidna_data.R
- Echidna_Internal_functions.R
- Echidna_other_functions.R
- Echidna_simulate_repertoire.R
- Echidna_vae_generate.R
- Echidna_vae_internal_functions.R
- GEX_clonotype.R
- GEX_cluster_genes.R
- GEX_cluster_genes_heatmap.R
- GEX_cluster_membership.R
- GEX_coexpression_coefficient.R
- GEX_DEgenes.R
- GEX_DEgenes_persample.R
- GEX_dottile_plot.R
- GEX_gene_visualization.R
- GEX_GOterm.R
- GEX_GSEA.R
- GEX_heatmap.R
- GEX_lineage_trajectories.R
- GEX_pairwise_degs.R
- GEX_phenotype.R
- GEX_phenotype_per_clone.R
- GEX_projecTILS.R
- GEX_proportions_barplot.R
- GEX_pseudobulk.R
- GEX_pseudotime_trajectory_plot.R
- GEX_scatter_coexpression.R
- GEX_topN_DE_genes_per_cluster.R
- GEX_trajectories.R
- GEX_visualize_clones.R
- GEX_volcano.R
- PlatypusDB_AIRR_to_VGM.R
- PlatypusDB_fetch.R
- PlatypusDB_find_CDR3s.R
- PlatypusDB_list_projects.R
- PlatypusDB_load_from_disk.R
- PlatypusDB_VGM_to_AIRR.R
- PlatypusML_balance.R
- PlatypusML_classification.R
- PlatypusML_feature_extraction_GEX.R
- PlatypusML_feature_extraction_VDJ.R
- Platypus_data.R
- Spatial_celltype_plot.R
- Spatial_cluster.R
- Spatial_density_plot.R
- Spatial_evolution_of_clonotype_plot.R
- Spatial_marker_expression.R
- Spatial_module_expression.R
- Spatial_nb_SHM_compare_to_germline_plot.R
- Spatial_scaling_parameters.R
- Spatial_selection_expanded_clonotypes.R
- Spatial_selection_of_cells_on_image.R
- Spatial_VDJ_assignment.R
- Spatial_VDJ_plot.R
- Spatial_vgm_formation.R
- VDJ_abundances.R
- VDJ_alpha_beta_Vgene_circos.R
- VDJ_analyze.R
- VDJ_antigen_integrate.R
- VDJ_assemble_for_PnP.R
- VDJ_bulk_to_vgm.R
- VDJ_call_enclone.R
- VDJ_call_MIXCR.R
- VDJ_call_MIXCR_full.R
- VDJ_call_recon.R
- VDJ_circos.R
- VDJ_clonal_donut.R
- VDJ_clonal_expansion.R
- VDJ_clonal_expansion_abundances.R
- VDJ_clonal_lineages.R
- VDJ_clonotype.R
- VDJ_contigs_to_vgm.R
- VDJ_db_annotate.R
- VDJ_db_load.R
- VDJ_diversity.R
- VDJ_dublets.R
- VDJ_dynamics.R
- VDJ_enclone.R
- VDJ_expand_aberrants.R
- VDJ_extract_germline.R
- VDJ_get_public.R
- VDJ_GEX_clonal_lineage_clusters.R
- VDJ_GEX_clonotyme.R
- VDJ_GEX_clonotype_clusters_circos.R
- VDJ_GEX_expansion.R
- VDJ_GEX_integrate.R
- VDJ_GEX_matrix.R
- VDJ_GEX_overlay_clones.R
- VDJ_GEX_stats.R
- VDJ_isotypes_per_clone.R
- VDJ_kmers.R
- VDJ_logoplot_vector.R
- VDJ_network.R
- VDJ_ordination.R
- VDJ_overlap_heatmap.R
- VDJ_per_clone.R
- VDJ_phylogenetic_trees.R
- VDJ_phylogenetic_trees_plot.R
- VDJ_plot_SHM.R
- VDJ_public.R
- VDJ_rarefaction.R
- VDJ_reclonotype_list_arrange.R
- VDJ_select_clonotypes.R
- VDJ_structure_analysis.R
- VDJ_tree.R
- VDJ_variants_per_clone.R
- VDJ_Vgene_usage.R
- VDJ_Vgene_usage_barplot.R
- VDJ_Vgene_usage_stacked_barplot.R
- VDJ_VJ_usage_circos.R
- VGM_expanded_clones.R
- VGM_expand_featurebarcodes.R
- VGM_integrate.R
Selected R package: Platypus
Click on the specific functions, references or examples using the links on the left
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