Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Y | Z A acceleration() (in module dynamo.pl) (in module dynamo.vf) action() (in module dynamo.vf) add_edge() (dynamo.vf.vfGraph method) add_edges() (dynamo.vf.vfGraph method) add_experiment_info() (dynamo.pp.Preprocessor method) add_fixed_points() (dynamo.vf.FixedPoints method) add_vertex() (dynamo.vf.vfGraph method) add_vertices() (dynamo.vf.vfGraph method) adhesion() (dynamo.vf.vfGraph method) Adjacency() (dynamo.vf.vfGraph class method) alignment() (in module dynamo.vf) all_minimal_st_separators() (dynamo.vf.vfGraph method) all_st_cuts() (dynamo.vf.vfGraph method) all_st_mincuts() (dynamo.vf.vfGraph method) alpha() (dynamo.vf.vfGraph method) andecestor() (in module dynamo.pd) animate_fates() (in module dynamo.mv) Ao_pot_map() (in module dynamo.vf) arcPlot() (in module dynamo.pl) are_adjacent() (dynamo.vf.vfGraph method) are_connected() (dynamo.vf.vfGraph method) articulation_points() (dynamo.vf.vfGraph method) as_directed() (dynamo.vf.vfGraph method) as_undirected() (dynamo.vf.vfGraph method) assign_fixed_points() (dynamo.vf.BaseVectorField method) (dynamo.vf.SvcVectorField method) assign_fixedpoints() (in module dynamo.vf) assortativity() (dynamo.vf.vfGraph method) assortativity_degree() (dynamo.vf.vfGraph method) assortativity_nominal() (dynamo.vf.vfGraph method) Asymmetric_Preference() (dynamo.vf.vfGraph method) Atlas() (dynamo.vf.vfGraph method) attributes() (dynamo.vf.vfGraph method) authority_score() (dynamo.vf.vfGraph method) automorphism_group() (dynamo.vf.vfGraph method) average_path_length() (dynamo.vf.vfGraph method) B Barabasi() (dynamo.vf.vfGraph method) BaseVectorField (class in dynamo.vf) basic_stats() (in module dynamo.pl) betweenness() (dynamo.vf.vfGraph method) bfs() (dynamo.vf.vfGraph method) bfsiter() (dynamo.vf.vfGraph method) Biadjacency() (dynamo.vf.vfGraph class method) bibcoupling() (dynamo.vf.vfGraph method) biconnected_components() (dynamo.vf.vfGraph method) Bipartite() (dynamo.vf.vfGraph class method) bipartite_projection() (dynamo.vf.vfGraph method) bipartite_projection_size() (dynamo.vf.vfGraph method) biplot() (in module dynamo.pl) blocks() (dynamo.vf.vfGraph method) BM() (in module dynamo.sample_data) bridges() (dynamo.vf.vfGraph method) bubble() (in module dynamo.pl) build_graph() (dynamo.vf.vfGraph method) C canonical_permutation() (dynamo.vf.vfGraph method) causality() (in module dynamo.pl) cell_accelerations() (in module dynamo.vf) cell_curvatures() (in module dynamo.vf) cell_cycle_scores() (in module dynamo.pl) cell_growth_rate() (in module dynamo.tl) cell_velocities() (in module dynamo.tl) cell_wise_confidence() (in module dynamo.tl) cell_wise_vectors() (in module dynamo.pl) cell_wise_vectors_3d() (in module dynamo.pl) chordal_completion() (dynamo.vf.vfGraph method) chromaffin() (in module dynamo.sample_data) Chung_Lu() (dynamo.vf.vfGraph method) circosPlot() (in module dynamo.pl) circosPlotDeprecated() (in module dynamo.pl) cleanup() (in module dynamo) clear() (dynamo.vf.vfGraph method) clique_number() (dynamo.vf.vfGraph method) cliques() (dynamo.vf.vfGraph method) closeness() (dynamo.vf.vfGraph method) cluster_field() (in module dynamo.vf) clusters() (dynamo.vf.vfGraph method) cocitation() (dynamo.vf.vfGraph method) coexp_measure() (in module dynamo.ext) cohesion() (dynamo.vf.vfGraph method) cohesive_blocks() (dynamo.vf.vfGraph method) comb_logic() (in module dynamo.pl) community_edge_betweenness() (dynamo.vf.vfGraph method) community_fastgreedy() (dynamo.vf.vfGraph method) community_fluid_communities() (dynamo.vf.vfGraph method) community_infomap() (dynamo.vf.vfGraph method) community_label_propagation() (dynamo.vf.vfGraph method) community_leading_eigenvector() (dynamo.vf.vfGraph method) community_leiden() (dynamo.vf.vfGraph method) community_multilevel() (dynamo.vf.vfGraph method) community_optimal_modularity() (dynamo.vf.vfGraph method) community_spinglass() (dynamo.vf.vfGraph method) community_voronoi() (dynamo.vf.vfGraph method) community_walktrap() (dynamo.vf.vfGraph method) complementer() (dynamo.vf.vfGraph method) components() (dynamo.vf.vfGraph method) compose() (dynamo.vf.vfGraph method) compute_acceleration() (dynamo.vf.SvcVectorField method) compute_curl() (dynamo.vf.SvcVectorField method) compute_curvature() (dynamo.vf.SvcVectorField method) compute_divergence() (dynamo.vf.SvcVectorField method) compute_eigvals() (dynamo.vf.FixedPoints method) compute_sensitivity() (dynamo.vf.SvcVectorField method) compute_torsion() (dynamo.vf.SvcVectorField method) confident_cell_velocities() (in module dynamo.tl) config_monocle_pearson_residuals_recipe() (dynamo.pp.Preprocessor method) config_monocle_recipe() (dynamo.pp.Preprocessor method) config_pearson_residuals_recipe() (dynamo.pp.Preprocessor method) config_sctransform_recipe() (dynamo.pp.Preprocessor method) config_seurat_recipe() (dynamo.pp.Preprocessor method) connected_components() (dynamo.vf.vfGraph method) constraint() (dynamo.vf.vfGraph method) construct_graph() (dynamo.vf.BaseVectorField method) (dynamo.vf.SvcVectorField method) contract_vertices() (dynamo.vf.vfGraph method) convergence_degree() (dynamo.vf.vfGraph method) convergence_field_size() (dynamo.vf.vfGraph method) convert_to_class() (dynamo.vf.vfGraph class method) converter() (in module dynamo.tl) copy() (dynamo.vf.vfGraph method) coreness() (dynamo.vf.vfGraph method) count_automorphisms() (dynamo.vf.vfGraph method) count_automorphisms_vf2() (dynamo.vf.vfGraph method) count_isomorphisms_vf2() (dynamo.vf.vfGraph method) count_multiple() (dynamo.vf.vfGraph method) count_subisomorphisms_vf2() (dynamo.vf.vfGraph method) curl() (in module dynamo.pl) (in module dynamo.vf) curvature() (in module dynamo.pl) (in module dynamo.vf) cut_vertices() (dynamo.vf.vfGraph method) D DataFrame() (dynamo.vf.vfGraph class method) ddhodge() (in module dynamo.ext) DDRTree() (in module dynamo.tl) De_Bruijn() (dynamo.vf.vfGraph method) decompose() (dynamo.vf.vfGraph method) degree() (dynamo.vf.vfGraph method) degree_distribution() (dynamo.vf.vfGraph method) Degree_Sequence() (dynamo.vf.vfGraph method) delete_edges() (dynamo.vf.vfGraph method) delete_vertices() (dynamo.vf.vfGraph method) density() (dynamo.vf.vfGraph method) DentateGyrus() (in module dynamo.sample_data) DentateGyrus_scvelo() (in module dynamo.sample_data) dfs() (dynamo.vf.vfGraph method) dfsiter() (dynamo.vf.vfGraph method) diameter() (dynamo.vf.vfGraph method) DictDict() (dynamo.vf.vfGraph class method) DictList() (dynamo.vf.vfGraph class method) difference() (dynamo.vf.vfGraph method) diffusion() (in module dynamo.tl) DiffusionMatrix() (in module dynamo.vf) diffusionMatrix() (in module dynamo.vf) disjoint_union() (dynamo.vf.vfGraph method) distances() (dynamo.vf.vfGraph method) divergence() (in module dynamo.pl) (in module dynamo.vf) diversity() (dynamo.vf.vfGraph method) dominator() (dynamo.vf.vfGraph method) dyad_census() (dynamo.vf.vfGraph method) dynamics() (in module dynamo.pl) (in module dynamo.tl) E eccentricity() (dynamo.vf.vfGraph method) ecount() (dynamo.vf.vfGraph method) edge_attributes() (dynamo.vf.vfGraph method) edge_betweenness() (dynamo.vf.vfGraph method) edge_connectivity() (dynamo.vf.vfGraph method) edge_disjoint_paths() (dynamo.vf.vfGraph method) eigen_adjacency() (dynamo.vf.vfGraph method) eigenvector_centrality() (dynamo.vf.vfGraph method) enrichr() (in module dynamo.ext) Erdos_Renyi() (dynamo.vf.vfGraph method) es (dynamo.vf.vfGraph attribute) Establishment() (dynamo.vf.vfGraph method) evaluate() (dynamo.vf.SvcVectorField method) (in module dynamo.sim) evcent() (dynamo.vf.vfGraph method) exp_by_groups() (in module dynamo.pl) expected_return_time() (in module dynamo.tl) F Famous() (dynamo.vf.vfGraph method) farthest_points() (dynamo.vf.vfGraph method) fate() (in module dynamo.pd) (in module dynamo.pl) fate_bias() (in module dynamo.pd) (in module dynamo.pl) feature_genes() (in module dynamo.pl) feedback_arc_set() (dynamo.vf.vfGraph method) feedback_vertex_set() (dynamo.vf.vfGraph method) filter_cells() (in module dynamo.pp) filter_cells_by_highly_variable_genes() (in module dynamo.pp) filter_cells_by_outliers() (in module dynamo.pp) filter_genes() (in module dynamo.pp) filter_genes_by_clusters() (in module dynamo.pp) filter_genes_by_outliers() (in module dynamo.pp) filter_genes_by_pattern() (in module dynamo.pp) find_fixed_points() (dynamo.vf.BaseVectorField method) (dynamo.vf.SvcVectorField method) find_group_markers() (in module dynamo.tl) FixedPoints (class in dynamo.vf) Forest_Fire() (dynamo.vf.vfGraph method) Formula() (dynamo.vf.vfGraph class method) from_adata() (dynamo.vf.BaseVectorField method) (dynamo.vf.SvcVectorField method) from_graph_tool() (dynamo.vf.vfGraph class method) from_networkx() (dynamo.vf.vfGraph class method) Full() (dynamo.vf.vfGraph method) Full_Bipartite() (dynamo.vf.vfGraph class method) Full_Citation() (dynamo.vf.vfGraph method) fundamental_cycles() (dynamo.vf.vfGraph method) G gen_fixed_points() (in module dynamo.vf) gen_gradient() (in module dynamo.vf) gene_wise_confidence() (in module dynamo.tl) generalized_diffusion_map() (in module dynamo.tl) get_adjacency() (dynamo.vf.vfGraph method) get_adjacency_sparse() (dynamo.vf.vfGraph method) get_adjlist() (dynamo.vf.vfGraph method) get_all_dependencies_version() (in module dynamo) get_all_shortest_paths() (dynamo.vf.vfGraph method) get_all_simple_paths() (dynamo.vf.vfGraph method) get_automorphisms_vf2() (dynamo.vf.vfGraph method) get_biadjacency() (dynamo.vf.vfGraph method) get_data() (dynamo.vf.BaseVectorField method) (dynamo.vf.SvcVectorField method) get_diameter() (dynamo.vf.vfGraph method) get_edge_dataframe() (dynamo.vf.vfGraph method) get_edgelist() (dynamo.vf.vfGraph method) get_eid() (dynamo.vf.vfGraph method) get_eids() (dynamo.vf.vfGraph method) get_fixed_point_types() (dynamo.vf.FixedPoints method) get_fixed_points() (dynamo.vf.BaseVectorField method) (dynamo.vf.SvcVectorField method) get_Hessian() (dynamo.vf.SvcVectorField method) get_incidence() (dynamo.vf.vfGraph method) get_inclist() (dynamo.vf.vfGraph method) get_init_path() (in module dynamo.pd) get_isomorphisms_vf2() (dynamo.vf.vfGraph method) get_J() (dynamo.vf.FixedPoints method) get_Jacobian() (dynamo.vf.SvcVectorField method) get_k_shortest_paths() (dynamo.vf.vfGraph method) get_Laplacian() (dynamo.vf.SvcVectorField method) get_shortest_path() (dynamo.vf.vfGraph method) get_shortest_path_astar() (dynamo.vf.vfGraph method) get_shortest_paths() (dynamo.vf.vfGraph method) get_subisomorphisms_lad() (dynamo.vf.vfGraph method) get_subisomorphisms_vf2() (dynamo.vf.vfGraph method) get_V() (dynamo.vf.BaseVectorField method) (dynamo.vf.SvcVectorField method) get_vertex_dataframe() (dynamo.vf.vfGraph method) get_X() (dynamo.vf.BaseVectorField method) (dynamo.vf.FixedPoints method) (dynamo.vf.SvcVectorField method) Gillespie() (in module dynamo.sim) girth() (dynamo.vf.vfGraph method) glm_degs() (in module dynamo.tl) gomory_hu_tree() (dynamo.vf.vfGraph method) graphize_vecfld() (in module dynamo.vf) GRG() (dynamo.vf.vfGraph class method) grid_vectors() (in module dynamo.pl) Growing_Random() (dynamo.vf.vfGraph method) H Haber() (in module dynamo.sample_data) harmonic_centrality() (dynamo.vf.vfGraph method) has_multiple() (dynamo.vf.vfGraph method) hdbscan() (in module dynamo.tl) hematopoiesis() (in module dynamo.sample_data) hematopoiesis_raw() (in module dynamo.sample_data) Hexagonal_Lattice() (dynamo.vf.vfGraph method) hgForebrainGlutamatergic() (in module dynamo.sample_data) highest_frac_genes() (in module dynamo.pl) (in module dynamo.pp) hivePlot() (in module dynamo.pl) hub_score() (dynamo.vf.vfGraph method) Hypercube() (dynamo.vf.vfGraph method) I Incidence() (dynamo.vf.vfGraph class method) incident() (dynamo.vf.vfGraph method) indegree() (dynamo.vf.vfGraph method) independence_number() (dynamo.vf.vfGraph method) independent_vertex_sets() (dynamo.vf.vfGraph method) induced_subgraph() (dynamo.vf.vfGraph method) infomap() (in module dynamo.pl) integrate() (dynamo.vf.BaseVectorField method) (dynamo.vf.SvcVectorField method) intersection() (dynamo.vf.vfGraph method) IntGrad() (in module dynamo.vf) is_acyclic() (dynamo.vf.vfGraph method) is_biconnected() (dynamo.vf.vfGraph method) is_bipartite() (dynamo.vf.vfGraph method) is_chordal() (dynamo.vf.vfGraph method) is_clique() (dynamo.vf.vfGraph method) is_complete() (dynamo.vf.vfGraph method) is_connected() (dynamo.vf.vfGraph method) is_dag() (dynamo.vf.vfGraph method) is_directed() (dynamo.vf.vfGraph method) is_independent_vertex_set() (dynamo.vf.vfGraph method) is_loop() (dynamo.vf.vfGraph method) is_minimal_separator() (dynamo.vf.vfGraph method) is_multiple() (dynamo.vf.vfGraph method) is_mutual() (dynamo.vf.vfGraph method) is_named() (dynamo.vf.vfGraph method) is_saddle() (dynamo.vf.FixedPoints method) is_separator() (dynamo.vf.vfGraph method) is_simple() (dynamo.vf.vfGraph method) is_stable() (dynamo.vf.FixedPoints method) is_tree() (dynamo.vf.vfGraph method) is_weighted() (dynamo.vf.vfGraph method) Isoclass() (dynamo.vf.vfGraph method) isoclass() (dynamo.vf.vfGraph method) isomorphic() (dynamo.vf.vfGraph method) isomorphic_bliss() (dynamo.vf.vfGraph method) isomorphic_vf2() (dynamo.vf.vfGraph method) J jacobian() (in module dynamo.pl) (in module dynamo.vf) jacobian_heatmap() (in module dynamo.pl) jacobian_kinetics() (in module dynamo.pl) K k_core() (dynamo.vf.vfGraph method) K_Regular() (dynamo.vf.vfGraph method) Kautz() (dynamo.vf.vfGraph method) kinetic_curves() (in module dynamo.pl) kinetic_heatmap() (in module dynamo.pl) knn() (dynamo.vf.vfGraph method) KO() (in module dynamo.pd) L lap_min_time() (in module dynamo.pl) laplacian() (dynamo.vf.vfGraph method) largest_cliques() (dynamo.vf.vfGraph method) largest_independent_vertex_sets() (dynamo.vf.vfGraph method) Lattice() (dynamo.vf.vfGraph method) layout() (dynamo.vf.vfGraph method) layout_auto() (dynamo.vf.vfGraph method) layout_bipartite() (dynamo.vf.vfGraph method) layout_circle() (dynamo.vf.vfGraph method) layout_davidson_harel() (dynamo.vf.vfGraph method) layout_drl() (dynamo.vf.vfGraph method) layout_fruchterman_reingold() (dynamo.vf.vfGraph method) layout_fruchterman_reingold_3d() (dynamo.vf.vfGraph method) layout_graphopt() (dynamo.vf.vfGraph method) layout_grid() (dynamo.vf.vfGraph method) layout_grid_3d() (dynamo.vf.vfGraph method) layout_kamada_kawai() (dynamo.vf.vfGraph method) layout_kamada_kawai_3d() (dynamo.vf.vfGraph method) layout_lgl() (dynamo.vf.vfGraph method) layout_mds() (dynamo.vf.vfGraph method) layout_random() (dynamo.vf.vfGraph method) layout_random_3d() (dynamo.vf.vfGraph method) layout_reingold_tilford() (dynamo.vf.vfGraph method) layout_reingold_tilford_circular() (dynamo.vf.vfGraph method) layout_sphere() (dynamo.vf.vfGraph method) layout_star() (dynamo.vf.vfGraph method) layout_sugiyama() (dynamo.vf.vfGraph method) layout_umap() (dynamo.vf.vfGraph method) LCF() (dynamo.vf.vfGraph method) least_action() (in module dynamo.pd) leiden() (in module dynamo.pl) (in module dynamo.tl) line_integral_conv() (in module dynamo.pl) linegraph() (dynamo.vf.vfGraph method) list_triangles() (dynamo.vf.vfGraph method) ListDict() (dynamo.vf.vfGraph class method) Load() (dynamo.vf.vfGraph class method) loading() (in module dynamo.pl) log1p() (in module dynamo.pp) louvain() (in module dynamo.pl) (in module dynamo.tl) M maxdegree() (dynamo.vf.vfGraph method) maxflow() (dynamo.vf.vfGraph method) maxflow_value() (dynamo.vf.vfGraph method) maximal_cliques() (dynamo.vf.vfGraph method) maximal_independent_vertex_sets() (dynamo.vf.vfGraph method) maximum_bipartite_matching() (dynamo.vf.vfGraph method) maximum_cardinality_search() (dynamo.vf.vfGraph method) mean_degree() (dynamo.vf.vfGraph method) MFPT() (in module dynamo.vf) mincut() (dynamo.vf.vfGraph method) mincut_value() (dynamo.vf.vfGraph method) minimum_cycle_basis() (dynamo.vf.vfGraph method) minimum_size_separators() (dynamo.vf.vfGraph method) mnn() (in module dynamo.tl) modularity() (dynamo.vf.vfGraph method) modularity_matrix() (dynamo.vf.vfGraph method) moments() (in module dynamo.tl) moran_i() (in module dynamo.tl) motifs_randesu() (dynamo.vf.vfGraph method) motifs_randesu_estimate() (dynamo.vf.vfGraph method) motifs_randesu_no() (dynamo.vf.vfGraph method) multimaxflow() (dynamo.vf.vfGraph method) N Nearest_Neighbor_Graph() (dynamo.vf.vfGraph method) neighborhood() (dynamo.vf.vfGraph method) neighborhood_size() (dynamo.vf.vfGraph method) neighbors() (dynamo.vf.vfGraph method) (in module dynamo.tl) nneighbors() (in module dynamo.pl) normalize_cell_expr_by_size_factors() (in module dynamo.pp) O omega() (dynamo.vf.vfGraph method) outdegree() (dynamo.vf.vfGraph method) P pagerank() (dynamo.vf.vfGraph method) pancreatic_endocrinogenesis() (in module dynamo.sample_data) path_integral() (in module dynamo.vf) path_length_hist() (dynamo.vf.vfGraph method) pca() (in module dynamo.pl) (in module dynamo.pp) permute_vertices() (dynamo.vf.vfGraph method) personalized_pagerank() (dynamo.vf.vfGraph method) perturbation() (in module dynamo.pd) phase_portraits() (in module dynamo.pl) plot_3d_streamtube() (in module dynamo.pl) plot_energy() (dynamo.vf.SvcVectorField method) (in module dynamo.pl) plot_fixed_points() (in module dynamo.pl) plot_fixed_points_2d() (in module dynamo.pl) plot_flow_field() (in module dynamo.pl) plot_hill_function() (in module dynamo.pl) plot_nullclines() (in module dynamo.pl) plot_separatrix() (in module dynamo.pl) plot_traj() (in module dynamo.pl) Potential() (in module dynamo.vf) predecessors() (dynamo.vf.vfGraph method) Preference() (dynamo.vf.vfGraph method) preprocess_adata() (dynamo.pp.Preprocessor method) preprocess_adata_monocle() (dynamo.pp.Preprocessor method) preprocess_adata_monocle_pearson_residuals() (dynamo.pp.Preprocessor method) preprocess_adata_pearson_residuals() (dynamo.pp.Preprocessor method) preprocess_adata_sctransform() (dynamo.pp.Preprocessor method) preprocess_adata_seurat() (dynamo.pp.Preprocessor method) preprocess_adata_seurat_wo_pca() (dynamo.pp.Preprocessor method) Preprocessor (class in dynamo.pp) Prufer() (dynamo.vf.vfGraph method) pseudotime_velocity() (in module dynamo.tl) psl() (in module dynamo.tl) R radius() (dynamo.vf.vfGraph method) Random_Bipartite() (dynamo.vf.vfGraph class method) random_walk() (dynamo.vf.vfGraph method) rank_acceleration_genes() (in module dynamo.vf) rank_curvature_genes() (in module dynamo.vf) rank_divergence_genes() (in module dynamo.vf) rank_expression_genes() (in module dynamo.vf) rank_genes() (in module dynamo.vf) rank_jacobian_genes() (in module dynamo.vf) rank_perturbation_cell_clusters() (in module dynamo.pd) rank_perturbation_cells() (in module dynamo.pd) rank_perturbation_genes() (in module dynamo.pd) rank_s_divergence_genes() (in module dynamo.vf) rank_sensitivity_genes() (in module dynamo.vf) rank_velocity_genes() (in module dynamo.vf) Read() (dynamo.vf.vfGraph class method) read() (in module dynamo) Read_Adjacency() (dynamo.vf.vfGraph class method) Read_DIMACS() (dynamo.vf.vfGraph class method) Read_DL() (dynamo.vf.vfGraph method) Read_Edgelist() (dynamo.vf.vfGraph method) Read_GML() (dynamo.vf.vfGraph method) Read_GraphDB() (dynamo.vf.vfGraph method) Read_GraphML() (dynamo.vf.vfGraph method) Read_GraphMLz() (dynamo.vf.vfGraph class method) read_h5ad() (in module dynamo) Read_Lgl() (dynamo.vf.vfGraph method) read_loom() (in module dynamo) Read_Ncol() (dynamo.vf.vfGraph method) Read_Pajek() (dynamo.vf.vfGraph method) Read_Pickle() (dynamo.vf.vfGraph class method) Read_Picklez() (dynamo.vf.vfGraph class method) Realize_Bipartite_Degree_Sequence() (dynamo.vf.vfGraph method) Realize_Degree_Sequence() (dynamo.vf.vfGraph method) Recent_Degree() (dynamo.vf.vfGraph method) recipe_deg_data() (in module dynamo.tl) recipe_kin_data() (in module dynamo.tl) recipe_mix_kin_deg_data() (in module dynamo.tl) recipe_monocle() (in module dynamo.pp) recipe_one_shot_data() (in module dynamo.tl) recipe_velocyto() (in module dynamo.pp) reciprocity() (dynamo.vf.vfGraph method) reduceDimension() (in module dynamo.tl) response() (in module dynamo.pl) reverse_edges() (dynamo.vf.vfGraph method) rewire() (dynamo.vf.vfGraph method) rewire_edges() (dynamo.vf.vfGraph method) Ring() (dynamo.vf.vfGraph method) run_scvelo() (in module dynamo.tl) run_velocyto() (in module dynamo.tl) S save() (dynamo.vf.vfGraph method) save_fig() (in module dynamo.pl) SBM() (dynamo.vf.vfGraph method) scale() (in module dynamo.pp) scatters() (in module dynamo.pl) scc() (in module dynamo.tl) scEU_seq_organoid() (in module dynamo.sample_data) scEU_seq_rpe1() (in module dynamo.sample_data) scifate_glmnet() (in module dynamo.ext) scNT_seq_neuron_labeling() (in module dynamo.sample_data) scNT_seq_neuron_splicing() (in module dynamo.sample_data) score_cells() (in module dynamo.tl) scribe() (in module dynamo.ext) select_genes_by_pearson_residuals() (in module dynamo.pp) select_genes_monocle() (in module dynamo.pp) sensitivity() (in module dynamo.pl) (in module dynamo.vf) sensitivity_heatmap() (in module dynamo.pl) sensitivity_kinetics() (in module dynamo.pl) set_figure_params() (in module dynamo.configuration) set_pub_style() (in module dynamo.configuration) shell_index() (dynamo.vf.vfGraph method) shortest_paths() (dynamo.vf.vfGraph method) shortest_paths_dijkstra() (dynamo.vf.vfGraph method) show_fraction() (in module dynamo.pl) show_landscape() (in module dynamo.pl) similarity_dice() (dynamo.vf.vfGraph method) similarity_inverse_log_weighted() (dynamo.vf.vfGraph method) similarity_jaccard() (dynamo.vf.vfGraph method) simple_cycles() (dynamo.vf.vfGraph method) simplify() (dynamo.vf.vfGraph method) Simulator() (in module dynamo.sim) solveQ() (in module dynamo.vf) space() (in module dynamo.pl) spanning_tree() (dynamo.vf.vfGraph method) SparseVFC() (in module dynamo.vf) speed() (in module dynamo.pl) (in module dynamo.vf) st_mincut() (dynamo.vf.vfGraph method) standardize_adata() (dynamo.pp.Preprocessor method) Star() (dynamo.vf.vfGraph method) state_graph() (in module dynamo.pd) (in module dynamo.pl) state_space_sampler() (in module dynamo.sim) Static_Fitness() (dynamo.vf.vfGraph method) Static_Power_Law() (dynamo.vf.vfGraph method) stationary_distribution() (in module dynamo.tl) streamline_clusters() (in module dynamo.pl) (in module dynamo.vf) streamline_plot() (in module dynamo.pl) strength() (dynamo.vf.vfGraph method) subcomponent() (dynamo.vf.vfGraph method) subgraph() (dynamo.vf.vfGraph method) subgraph_edges() (dynamo.vf.vfGraph method) subisomorphic_lad() (dynamo.vf.vfGraph method) subisomorphic_vf2() (dynamo.vf.vfGraph method) successors() (dynamo.vf.vfGraph method) summary() (dynamo.vf.vfGraph method) SvcVectorField (class in dynamo.vf) T to_dict_dict() (dynamo.vf.vfGraph method) to_dict_list() (dynamo.vf.vfGraph method) to_directed() (dynamo.vf.vfGraph method) to_graph_tool() (dynamo.vf.vfGraph method) to_list_dict() (dynamo.vf.vfGraph method) to_networkx() (dynamo.vf.vfGraph method) to_prufer() (dynamo.vf.vfGraph method) to_tuple_list() (dynamo.vf.vfGraph method) to_undirected() (dynamo.vf.vfGraph method) toggle() (in module dynamo.sim) top_n_markers() (in module dynamo.tl) topography() (in module dynamo.pl) (in module dynamo.vf) topological_sorting() (dynamo.vf.vfGraph method) torsion() (in module dynamo.vf) train() (dynamo.vf.SvcVectorField method) transition_rate() (in module dynamo.vf) transitivity_avglocal_undirected() (dynamo.vf.vfGraph method) transitivity_local_undirected() (dynamo.vf.vfGraph method) transitivity_undirected() (dynamo.vf.vfGraph method) Tree() (dynamo.vf.vfGraph method) Tree_Game() (dynamo.vf.vfGraph method) tree_model() (in module dynamo.pd) triad_census() (dynamo.vf.vfGraph method) Triangular_Lattice() (dynamo.vf.vfGraph method) trimap() (in module dynamo.pl) tsne() (in module dynamo.pl) TupleList() (dynamo.vf.vfGraph class method) two_groups_degs() (in module dynamo.tl) U umap() (in module dynamo.pl) unfold_tree() (dynamo.vf.vfGraph method) union() (dynamo.vf.vfGraph method) V variance_explained() (in module dynamo.pl) vcount() (dynamo.vf.vfGraph method) vector_field_function() (in module dynamo.vf) VectorField() (in module dynamo.vf) velocities() (in module dynamo.vf) velocity_N() (in module dynamo.tl) vertex_attributes() (dynamo.vf.vfGraph method) vertex_coloring_greedy() (dynamo.vf.vfGraph method) vertex_connectivity() (dynamo.vf.vfGraph method) vertex_disjoint_paths() (dynamo.vf.vfGraph method) vfGraph (class in dynamo.vf) vlm_to_adata() (in module dynamo.tl) vs (dynamo.vf.vfGraph attribute) W Wang_action() (in module dynamo.vf) Wang_LAP() (in module dynamo.vf) Watts_Strogatz() (dynamo.vf.vfGraph method) Weighted_Adjacency() (dynamo.vf.vfGraph class method) write() (dynamo.vf.vfGraph method) write_adjacency() (dynamo.vf.vfGraph method) write_dimacs() (dynamo.vf.vfGraph method) write_dot() (dynamo.vf.vfGraph method) write_edgelist() (dynamo.vf.vfGraph method) write_gml() (dynamo.vf.vfGraph method) write_graphml() (dynamo.vf.vfGraph method) write_graphmlz() (dynamo.vf.vfGraph method) write_leda() (dynamo.vf.vfGraph method) write_lgl() (dynamo.vf.vfGraph method) write_ncol() (dynamo.vf.vfGraph method) write_pajek() (dynamo.vf.vfGraph method) write_pickle() (dynamo.vf.vfGraph method) write_picklez() (dynamo.vf.vfGraph method) write_svg() (dynamo.vf.vfGraph method) Y Ying_model() (in module dynamo.sim) Z zebrafish() (in module dynamo.sample_data)