Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W _ __contains__() (netflow.keepers.keeper.DataKeeper method) (netflow.keepers.keeper.DistanceKeeper method) (netflow.keepers.keeper.GraphKeeper method) __detect_branching_haghverdi16() (netflow.pose.organization.POSER method) __getitem__() (netflow.keepers.keeper.DataKeeper method) (netflow.keepers.keeper.DistanceKeeper method) (netflow.keepers.keeper.GraphKeeper method) __init__() (netflow.keepers.keeper.DataKeeper method) (netflow.keepers.keeper.DataView method) (netflow.keepers.keeper.DistanceKeeper method) (netflow.keepers.keeper.DistanceView method) (netflow.keepers.keeper.GraphKeeper method) (netflow.keepers.keeper.Keeper method) (netflow.methods.classes.InfoNet method) (netflow.pose.organization.POSER method) (netflow.pose.organization.Tree method) (netflow.pose.organization.TreeNode method) __iter__() (netflow.keepers.keeper.DataKeeper method) (netflow.keepers.keeper.DistanceKeeper method) (netflow.keepers.keeper.GraphKeeper method) __module__ (netflow.keepers.keeper.DataKeeper attribute) (netflow.keepers.keeper.DataView attribute) (netflow.keepers.keeper.DistanceKeeper attribute) (netflow.keepers.keeper.DistanceView attribute) (netflow.keepers.keeper.GraphKeeper attribute) (netflow.keepers.keeper.Keeper attribute) (netflow.methods.classes.InfoNet attribute) (netflow.pose.organization.POSER attribute) (netflow.pose.organization.Tree attribute) (netflow.pose.organization.TreeNode attribute) __repr__() (netflow.pose.organization.TreeNode method) _branch_member_indices() (in module netflow.probe.visualization) _branch_member_labels() (in module netflow.probe.visualization) _branch_order() (in module netflow.probe.visualization) _check_num_observations() (netflow.keepers.keeper.Keeper method) _check_observation_labels() (netflow.keepers.keeper.Keeper method) _compute_transitions() (in module netflow.pose.organization) _construct_mst_topology() (netflow.pose.organization.POSER method) _construct_topology() (netflow.pose.organization.POSER method) _curve_sin() (in module netflow.probe.visualization) _curve_trace() (in module netflow.probe.visualization) _detect_branch() (netflow.pose.organization.POSER method) _detect_branching_single_haghverdi16() (netflow.pose.organization.POSER method) _detect_branching_single_wolf17_bi() (netflow.pose.organization.POSER method) _detect_branching_single_wolf17_tri() (netflow.pose.organization.POSER method) _distance_to_similarity() (in module netflow.pose.similarity) _dpt_from_augmented_sym_transitions() (in module netflow.pose.organization) _get_node_from_counter() (netflow.pose.organization.Tree method) _interbranch_edges() (in module netflow.probe.visualization) _kendall_tau_add() (netflow.pose.organization.POSER method) _kendall_tau_diff() (netflow.pose.organization.POSER method) _kendall_tau_subtract() (netflow.pose.organization.POSER method) _largest_branch() (in module netflow.probe.visualization) _neighboring_branches() (in module netflow.probe.visualization) _search_counter() (netflow.pose.organization.Tree method) _set_pseudo_dist() (netflow.pose.organization.POSER method) _sorted_members() (in module netflow.probe.visualization) _trace_sin() (in module netflow.probe.visualization) A add_child() (netflow.pose.organization.TreeNode method) add_data() (netflow.keepers.keeper.DataKeeper method) (netflow.keepers.keeper.DistanceKeeper method) (netflow.keepers.keeper.Keeper method) add_distance() (netflow.keepers.keeper.Keeper method) add_graph() (netflow.keepers.keeper.GraphKeeper method) (netflow.keepers.keeper.Keeper method) add_misc() (netflow.keepers.keeper.Keeper method) add_similarity() (netflow.keepers.keeper.Keeper method) add_stacked_data() (netflow.keepers.keeper.DistanceKeeper method) add_stacked_distance() (netflow.keepers.keeper.Keeper method) add_stacked_similarity() (netflow.keepers.keeper.Keeper method) all_data() (netflow.pose.organization.Tree method) alpha_numeric_sorted() (in module netflow.probe.visualization) anisotropic_laplacian_matrix() (netflow.methods.classes.InfoNet method) avg_cluster_edges() (in module netflow.probe.clustering) B branch_clustering() (in module netflow.probe.clustering) branchings_segments() (netflow.pose.organization.POSER method) C check_connected_graph() (in module netflow.checks) check_distance_matrix() (in module netflow.checks) check_edges_in_graph() (in module netflow.checks) check_graph_no_self_loops() (in module netflow.checks) check_graph_weights() (in module netflow.checks) check_matrix_no_nan() (in module netflow.checks) check_matrix_nonnegative() (in module netflow.checks) check_symmetric() (in module netflow.checks) clustermap() (in module netflow.utils) co_branch_indicator() (netflow.pose.organization.Tree method) compute_dpt_from_augmented_sym_transitions() (netflow.keepers.keeper.Keeper method) compute_dpt_from_similarity() (netflow.keepers.keeper.Keeper method) compute_edge_weights() (in module netflow.utils) compute_eigen() (in module netflow.utils) compute_graph_distances() (in module netflow.utils) (netflow.methods.classes.InfoNet method) compute_multiscale_VNE_transition_from_similarity() (netflow.keepers.keeper.Keeper method) compute_multiscale_VNE_transitions_from_similarity() (in module netflow.pose.organization) compute_pearson() (in module netflow.methods.stats) compute_pearson_parallel() (in module netflow.methods.stats) compute_rw_transitions() (in module netflow.pose.organization) compute_rw_transitions_from_similarity() (netflow.keepers.keeper.Keeper method) compute_sigmas() (netflow.keepers.keeper.Keeper method) compute_similarity_from_distance() (netflow.keepers.keeper.Keeper method) compute_spearman() (in module netflow.methods.stats) compute_spearman_parallel() (in module netflow.methods.stats) compute_sym_diffusion_affinity_transitions() (in module netflow.pose.organization) compute_transitions() (in module netflow.pose.organization) compute_transitions_from_similarity() (netflow.keepers.keeper.Keeper method) construct_anisotropic_laplacian_matrix() (in module netflow.utils) construct_pose() (netflow.keepers.keeper.Keeper method) construct_pose_mst_nn_topology() (netflow.pose.organization.POSER method) construct_pose_mst_topology() (netflow.pose.organization.POSER method) construct_pose_nn_topology() (netflow.pose.organization.POSER method) contains() (netflow.pose.organization.TreeNode method) convert_similarity_to_distance() (netflow.keepers.keeper.Keeper method) create_colorbar() (in module netflow.probe.jupyter_app) create_legend() (in module netflow.probe.jupyter_app) D data (netflow.keepers.keeper.DataKeeper property) (netflow.keepers.keeper.DataView property) (netflow.keepers.keeper.DistanceKeeper property) (netflow.keepers.keeper.DistanceView property) (netflow.keepers.keeper.Keeper property) DataKeeper (class in netflow.keepers.keeper) DataView (class in netflow.keepers.keeper) dbscan_clustering() (in module netflow.probe.clustering) density() (netflow.keepers.keeper.DistanceView method) depth() (netflow.pose.organization.TreeNode method) detect_branches() (netflow.pose.organization.POSER method) detect_branching() (netflow.pose.organization.POSER method) diffuse_multiple_profiles() (netflow.methods.classes.InfoNet method) diffuse_profile() (netflow.methods.classes.InfoNet method) disp() (netflow.pose.organization.Tree method) (netflow.pose.organization.TreeNode method) dispersion() (netflow.methods.classes.InfoNet method) dispersion_() (in module netflow.utils) distance_density() (netflow.keepers.keeper.Keeper method) distance_density_argmax() (netflow.keepers.keeper.Keeper method) distance_density_argmin() (netflow.keepers.keeper.Keeper method) distance_to_similarity() (in module netflow.pose.similarity) DistanceKeeper (class in netflow.keepers.keeper) distances (netflow.keepers.keeper.Keeper property) DistanceView (class in netflow.keepers.keeper) dotplot() (in module netflow.probe.visualization) dpt_from_augmented_sym_transitions() (in module netflow.pose.organization) E edges_from_mutual_knn_indices() (in module netflow.pose.similarity) euc_distance_pairwise_observation_feature_nbhd() (netflow.keepers.keeper.Keeper method) euc_distance_pairwise_observation_profile() (netflow.keepers.keeper.Keeper method) extract_branchings() (netflow.pose.organization.POSER method) F feature_index() (netflow.keepers.keeper.DataView method) feature_labels (netflow.keepers.keeper.DataView property) features_labels (netflow.keepers.keeper.DataKeeper property) find_knee_point() (in module netflow.utils) forceatlas2_layout() (in module netflow.probe.visualization) fuse_similarities() (netflow.keepers.keeper.Keeper method) G gauss_conv() (in module netflow.utils) gauss_window() (in module netflow.utils) get_edge_colors() (in module netflow.probe.jupyter_app) get_knn_indices_distances() (in module netflow.pose.similarity) get_leaves() (netflow.pose.organization.Tree method) get_leaves_indices() (netflow.pose.organization.Tree method) get_node() (netflow.pose.organization.Tree method) get_node_colors() (in module netflow.probe.jupyter_app) get_node_from_name() (netflow.pose.organization.Tree method) get_pose() (in module netflow.pose.organization) get_times() (in module netflow.utils) GraphKeeper (class in netflow.keepers.keeper) graphs (netflow.keepers.keeper.GraphKeeper property) (netflow.keepers.keeper.Keeper property) H heat_kernel() (in module netflow.utils) high_res_branch_graph() (in module netflow.probe.clustering) high_res_clustered_branch_graph() (in module netflow.probe.clustering) I identify_local_tips() (netflow.pose.organization.POSER method) InfoNet (class in netflow.methods.classes) insert() (netflow.pose.organization.Tree method) integrate_multiscale_VNE_transitions_from_similarities() (netflow.keepers.keeper.Keeper method) integrate_transitions() (netflow.keepers.keeper.Keeper method) integrate_transitions_from_similarity() (netflow.keepers.keeper.Keeper method) interaction_iterator() (in module netflow.utils) invariant_measure() (in module netflow.utils) invariant_measures() (netflow.methods.classes.InfoNet method) is_leaf() (netflow.pose.organization.TreeNode method) is_root() (netflow.pose.organization.TreeNode method) items() (netflow.keepers.keeper.DataKeeper method) (netflow.keepers.keeper.DistanceKeeper method) (netflow.keepers.keeper.GraphKeeper method) K Keeper (class in netflow.keepers.keeper) kendall_tau() (netflow.methods.classes.InfoNet method) kendall_tau_() (in module netflow.utils) kendall_tau_split() (netflow.pose.organization.POSER method) keys() (netflow.keepers.keeper.DataKeeper method) (netflow.keepers.keeper.DistanceKeeper method) (netflow.keepers.keeper.GraphKeeper method) KM_between_groups() (in module netflow.probe.visualization) L label (netflow.keepers.keeper.DataView property) (netflow.keepers.keeper.DistanceView property) load_data() (netflow.keepers.keeper.Keeper method) load_diffused_profile() (netflow.methods.classes.InfoNet method) load_diffused_timepoint_profile() (netflow.methods.classes.InfoNet method) load_distance() (netflow.keepers.keeper.Keeper method) load_graph() (netflow.keepers.keeper.Keeper method) load_similarity() (netflow.keepers.keeper.Keeper method) load_stacked_distance() (netflow.keepers.keeper.Keeper method) load_stacked_similarity() (netflow.keepers.keeper.Keeper method) log1p() (netflow.keepers.keeper.Keeper method) louvain() (in module netflow.probe.clustering) louvain_paritioned() (in module netflow.probe.clustering) M mann_whitney_u_test() (in module netflow.methods.stats) matplotlib_to_plotly_cmap() (in module netflow.probe.jupyter_app) max_depth() (netflow.pose.organization.Tree method) misc (netflow.keepers.keeper.Keeper property) module netflow netflow.checks netflow.keepers netflow.keepers.keeper netflow.methods netflow.methods.classes netflow.methods.metrics netflow.methods.stats netflow.pose netflow.pose.organization netflow.pose.similarity netflow.probe netflow.probe.clustering netflow.probe.jupyter_app netflow.probe.visualization netflow.utils multiple_pairwise_observation_neighborhood_euc_distance() (netflow.methods.classes.InfoNet method) multiple_pairwise_observation_neighborhood_wass_distance() (netflow.methods.classes.InfoNet method) mutual_knn_edges() (in module netflow.pose.similarity) mutual_knn_indices() (in module netflow.pose.similarity) N neighborhood() (netflow.methods.classes.InfoNet method) neighborhood_profiles() (netflow.methods.classes.InfoNet method) netflow module netflow.checks module netflow.keepers module netflow.keepers.keeper module netflow.methods module netflow.methods.classes module netflow.methods.metrics module netflow.methods.stats module netflow.pose module netflow.pose.organization module netflow.pose.similarity module netflow.probe module netflow.probe.clustering module netflow.probe.jupyter_app module netflow.probe.visualization module netflow.utils module norm_features() (in module netflow.methods.metrics) norm_features_() (in module netflow.methods.metrics) norm_features_as_sym_dist() (in module netflow.methods.metrics) num_features (netflow.keepers.keeper.DataKeeper property) (netflow.keepers.keeper.DataView property) num_observations (netflow.keepers.keeper.DataKeeper property) (netflow.keepers.keeper.DataView property) (netflow.keepers.keeper.DistanceKeeper property) (netflow.keepers.keeper.DistanceView property) (netflow.keepers.keeper.Keeper property) nx_to_cytoscape() (in module netflow.probe.jupyter_app) O observation_index() (netflow.keepers.keeper.DataKeeper method) (netflow.keepers.keeper.DataView method) (netflow.keepers.keeper.DistanceKeeper method) (netflow.keepers.keeper.DistanceView method) (netflow.keepers.keeper.Keeper method) observation_labels (netflow.keepers.keeper.DataKeeper property) (netflow.keepers.keeper.DataView property) (netflow.keepers.keeper.DistanceKeeper property) (netflow.keepers.keeper.DistanceView property) (netflow.keepers.keeper.Keeper property) optimal_transportation_distance() (in module netflow.methods.metrics) OTD() (in module netflow.methods.metrics) P pairwise_observation_euc_distances() (in module netflow.methods.metrics) pairwise_observation_neighborhood_euc_distance() (netflow.methods.classes.InfoNet method) pairwise_observation_neighborhood_wass_distance() (netflow.methods.classes.InfoNet method) pairwise_observation_profile_euc_distance() (netflow.methods.classes.InfoNet method) pairwise_observation_profile_wass_distance() (netflow.methods.classes.InfoNet method) pairwise_observation_wass_distances() (in module netflow.methods.metrics) PCA() (netflow.keepers.keeper.Keeper method) perform_stat_test() (in module netflow.methods.stats) pij() (in module netflow.utils) plot_profiles() (netflow.methods.classes.InfoNet method) plot_topology() (in module netflow.probe.visualization) plot_topology2() (in module netflow.probe.visualization) POSER (class in netflow.pose.organization) R render_pose() (in module netflow.probe.jupyter_app) renderer() (in module netflow.probe.jupyter_app) root() (netflow.pose.organization.Tree method) root_max_ratio() (in module netflow.pose.organization) S save_data() (netflow.keepers.keeper.Keeper method) save_distance() (netflow.keepers.keeper.Keeper method) save_misc() (netflow.keepers.keeper.Keeper method) save_similarity() (netflow.keepers.keeper.Keeper method) search() (netflow.pose.organization.Tree method) search_data() (netflow.pose.organization.Tree method) select_segment() (netflow.pose.organization.POSER method) sigma_knn() (in module netflow.pose.similarity) sigma_knn_() (in module netflow.pose.similarity) similarities (netflow.keepers.keeper.Keeper property) similarity_density() (netflow.keepers.keeper.Keeper method) similarity_density_argmax() (netflow.keepers.keeper.Keeper method) sin_layout() (in module netflow.probe.visualization) single_branch() (netflow.pose.organization.POSER method) spearmanr() (netflow.methods.classes.InfoNet method) spearmanr_() (in module netflow.utils) stack_triu() (netflow.methods.classes.InfoNet method) stack_triu_() (in module netflow.utils) stack_triu_where() (netflow.methods.classes.InfoNet method) stack_triu_where_() (in module netflow.utils) standardize() (netflow.keepers.keeper.DataKeeper method) (netflow.keepers.keeper.DataView method) (netflow.keepers.keeper.Keeper method) stat_test() (in module netflow.methods.stats) subset() (netflow.keepers.keeper.DataKeeper method) (netflow.keepers.keeper.DataView method) (netflow.keepers.keeper.DistanceKeeper method) (netflow.keepers.keeper.DistanceView method) (netflow.keepers.keeper.Keeper method) T t_test() (in module netflow.methods.stats) to_frame() (netflow.keepers.keeper.DataView method) (netflow.keepers.keeper.DistanceView method) Tree (class in netflow.pose.organization) TreeNode (class in netflow.pose.organization) U unstack_triu_() (in module netflow.utils) V value_counter() (netflow.methods.classes.InfoNet method) von_neumann_entropy() (in module netflow.utils) W wass_distance() (in module netflow.methods.metrics) wass_distance_pairwise_observation_feature_nbhd() (netflow.keepers.keeper.Keeper method) wass_distance_pairwise_observation_profile() (netflow.keepers.keeper.Keeper method) wavy_curve_layout() (in module netflow.probe.visualization) weighted_observation_network() (netflow.methods.classes.InfoNet method) wilcoxon_signed_rank_test() (in module netflow.methods.stats)
