Index

A

act() (NORDic.NORDic_DR.bandits.AdaHedge method) (NORDic.NORDic_DR.bandits.Greedy method) (NORDic.NORDic_DR.bandits.Learner method) AdaHedge (class in NORDic.NORDic_DR.bandits) adaptive_testing() (in module NORDic.NORDic_DR.functions) add_initial_states() (NORDic.UTILS.utils_sim.BN_SIM method) (NORDic.UTILS.utils_sim.BONESIS_SIM method) (NORDic.UTILS.utils_sim.MABOSS_SIM method) (NORDic.UTILS.utils_sim.MPBN_SIM method) add_permanent_mutation() (NORDic.UTILS.utils_sim.BN_SIM method) (NORDic.UTILS.utils_sim.BONESIS_SIM method) (NORDic.UTILS.utils_sim.MABOSS_SIM method) (NORDic.UTILS.utils_sim.MPBN_SIM method)

add_transient_mutation() (NORDic.UTILS.utils_sim.BN_SIM method) (NORDic.UTILS.utils_sim.BONESIS_SIM method) (NORDic.UTILS.utils_sim.MABOSS_SIM method) (NORDic.UTILS.utils_sim.MPBN_SIM method) aggregate_networks() (in module NORDic.UTILS.utils_network) apply() (NORDic.NORDic_DR.bandits.LinGapE method) (NORDic.NORDic_DR.bandits.MisLid method) argmax_m() (in module NORDic.NORDic_DR.utils) attrs_similarity() (NORDic.UTILS.utils_sim.BN_SIM method)

B

barycentric_spanner() (in module NORDic.NORDic_DR.utils) baseline() (in module NORDic.NORDic_DS.functions) best_answer() (NORDic.NORDic_DR.bandits.MisLid method) binarize_experiments() (in module NORDic.UTILS.utils_state) binarize_via_CD() (in module NORDic.UTILS.LINCS_utils)

BN_SIM (class in NORDic.UTILS.utils_sim) BONESIS_SIM (class in NORDic.UTILS.utils_sim) boxplot() (NORDic.UTILS.utils_sim.BN_SIM method) build_influences() (in module NORDic.UTILS.utils_grn) build_observations() (in module NORDic.UTILS.utils_grn) build_url() (in module NORDic.UTILS.LINCS_utils)

C

c_kt() (in module NORDic.NORDic_DR.utils) capture() (in module NORDic.UTILS.utils_network) (in module NORDic.UTILS.utils_sim) Centr() (in module NORDic.UTILS.utils_grn) choice() (in module NORDic.UTILS.utils_sim) CL() (in module NORDic.UTILS.utils_grn) clear() (NORDic.NORDic_DR.bandits.Misspecified method) closest_alternative() (in module NORDic.NORDic_DR.utils) cnorm() (in module NORDic.NORDic_DR.utils) compare_states() (in module NORDic.UTILS.utils_state)

compute_drug_signatures_L1000() (in module NORDic.NORDic_DS.get_drug_signatures) compute_frontier() (in module NORDic.NORDic_DS.functions) compute_interference_scale() (in module NORDic.UTILS.LINCS_utils) compute_metrics() (in module NORDic.NORDic_DS.functions) compute_score() (in module NORDic.NORDic_DS.functions) compute_similarities() (in module NORDic.NORDic_PMR.functions) convert_ctrlgenes_EntrezGene() (in module NORDic.UTILS.LINCS_utils) convert_EntrezGene_LINCSL1000() (in module NORDic.UTILS.utils_data) convert_genes_EntrezGene() (in module NORDic.UTILS.utils_data) create_grn() (in module NORDic.UTILS.utils_grn) create_restricted_drug_signatures() (in module NORDic.UTILS.LINCS_utils)

D

desirability() (in module NORDic.UTILS.utils_grn) determine_edge_threshold() (in module NORDic.UTILS.utils_network) download_file() (in module NORDic.UTILS.LINCS_utils)

download_lincs_files() (in module NORDic.UTILS.LINCS_utils) drugname2pubchem() (in module NORDic.NORDic_DS.get_drug_signatures) DS() (in module NORDic.UTILS.utils_grn)

E

empirical_pvalue() (in module NORDic.NORDic_DS.functions) enumerate_attractors() (NORDic.UTILS.utils_sim.BN_SIM method) (NORDic.UTILS.utils_sim.BONESIS_SIM method) (NORDic.UTILS.utils_sim.MABOSS_SIM method) (NORDic.UTILS.utils_sim.MPBN_SIM method)

F

finetune_binthres() (in module NORDic.UTILS.utils_state)

G

gaussian() (in module NORDic.NORDic_DR.bandits) general_topological_parameter() (in module NORDic.UTILS.utils_grn) generate_trajectories() (NORDic.UTILS.utils_sim.BN_SIM method) (NORDic.UTILS.utils_sim.BONESIS_SIM method) (NORDic.UTILS.utils_sim.MABOSS_SIM method) (NORDic.UTILS.utils_sim.MPBN_SIM method) get_all_celllines() (in module NORDic.UTILS.utils_data) get_app_name_STRING() (in module NORDic.UTILS.STRING_utils) get_experimental_constraints() (in module NORDic.UTILS.utils_exp) get_genes_downstream() (in module NORDic.UTILS.utils_grn) get_genes_evidences_from_DISGENET() (in module NORDic.UTILS.DISGENET_utils) get_genes_interactions_from_PPI() (in module NORDic.UTILS.utils_grn) get_genes_most_variable() (in module NORDic.UTILS.utils_grn) get_genes_proteins_from_DISGENET() (in module NORDic.UTILS.DISGENET_utils) get_grfs_from_solution() (in module NORDic.UTILS.utils_grn) get_image_from_STRING() (in module NORDic.UTILS.STRING_utils) get_interactions_from_STRING() (in module NORDic.UTILS.STRING_utils) get_interactions_partners_from_STRING() (in module NORDic.UTILS.STRING_utils)

get_maxdegree() (in module NORDic.UTILS.utils_grn) get_minimal_edges() (in module NORDic.UTILS.utils_grn) get_network_from_OmniPath() (in module NORDic.UTILS.utils_network) get_network_from_STRING() (in module NORDic.UTILS.STRING_utils) get_protein_names_from_STRING() (in module NORDic.UTILS.STRING_utils) get_ranking() (in module NORDic.NORDic_DS.get_drug_signatures) get_targets_DrugBank() (in module NORDic.NORDic_DS.get_drug_targets) get_targets_DrugCentral() (in module NORDic.NORDic_DS.get_drug_targets) get_targets_LINCS() (in module NORDic.NORDic_DS.get_drug_targets) get_targets_MINERVA() (in module NORDic.NORDic_DS.get_drug_targets) get_targets_TTD() (in module NORDic.NORDic_DS.get_drug_targets) get_treated_control_dataset() (in module NORDic.UTILS.LINCS_utils) get_user_key() (in module NORDic.UTILS.LINCS_utils) get_user_key_DISGENET() (in module NORDic.UTILS.DISGENET_utils) get_weakly_connected() (in module NORDic.UTILS.utils_grn) Greedy (class in NORDic.NORDic_DR.bandits) greedy() (in module NORDic.NORDic_PMR.functions) (NORDic.NORDic_DR.bandits.LinGapE method) GT() (in module NORDic.UTILS.utils_grn)

H

heuristic() (in module NORDic.NORDic_DR.bandits)

I

import_all_solutions() (in module NORDic.NORDic_NI.functions) incur() (NORDic.NORDic_DR.bandits.AdaHedge method) (NORDic.NORDic_DR.bandits.Greedy method) (NORDic.NORDic_DR.bandits.Learner method) infer_network() (in module NORDic.UTILS.utils_grn)

influences2graph() (in module NORDic.UTILS.utils_plot) initialize_network() (NORDic.UTILS.utils_sim.BN_SIM method) (NORDic.UTILS.utils_sim.BONESIS_SIM method) (NORDic.UTILS.utils_sim.MABOSS_SIM method) (NORDic.UTILS.utils_sim.MPBN_SIM method)

L

lambert() (in module NORDic.NORDic_DR.utils) Learner (class in NORDic.NORDic_DR.bandits)

LinGapE (class in NORDic.NORDic_DR.bandits) load_grn() (in module NORDic.UTILS.utils_grn)

M

MABOSS_SIM (class in NORDic.UTILS.utils_sim) mahalanobis() (in module NORDic.NORDic_DR.utils) merge_network_PPI() (in module NORDic.UTILS.utils_network) MisLid (class in NORDic.NORDic_DR.bandits) Misspecified (class in NORDic.NORDic_DR.bandits) misspecified() (in module NORDic.NORDic_DR.bandits) module NORDic.NORDic_DR.bandits NORDic.NORDic_DR.functions NORDic.NORDic_DR.utils NORDic.NORDic_DS.functions NORDic.NORDic_DS.get_drug_signatures NORDic.NORDic_DS.get_drug_targets NORDic.NORDic_NI.functions NORDic.NORDic_PMR.functions NORDic.UTILS.DISGENET_utils NORDic.UTILS.LINCS_utils NORDic.UTILS.STRING_utils NORDic.UTILS.utils_data NORDic.UTILS.utils_exp NORDic.UTILS.utils_grn NORDic.UTILS.utils_network NORDic.UTILS.utils_plot NORDic.UTILS.utils_sim NORDic.UTILS.utils_state

MPBN_SIM (class in NORDic.UTILS.utils_sim)

N

network_identification() (in module NORDic.NORDic_NI.functions) NORDic.NORDic_DR.bandits module NORDic.NORDic_DR.functions module NORDic.NORDic_DR.utils module NORDic.NORDic_DS.functions module NORDic.NORDic_DS.get_drug_signatures module NORDic.NORDic_DS.get_drug_targets module NORDic.NORDic_NI.functions module NORDic.NORDic_PMR.functions module NORDic.UTILS.DISGENET_utils module

NORDic.UTILS.LINCS_utils module NORDic.UTILS.STRING_utils module NORDic.UTILS.utils_data module NORDic.UTILS.utils_exp module NORDic.UTILS.utils_grn module NORDic.UTILS.utils_network module NORDic.UTILS.utils_plot module NORDic.UTILS.utils_sim module NORDic.UTILS.utils_state module

O

optimistic_gradient() (in module NORDic.NORDic_DR.utils)

optimized() (NORDic.NORDic_DR.bandits.LinGapE method)

P

plot_boxplots() (in module NORDic.UTILS.utils_plot) plot_discrete_distributions() (in module NORDic.UTILS.utils_plot) plot_distributions() (in module NORDic.UTILS.utils_plot) plot_heatmap() (in module NORDic.UTILS.utils_plot) plot_influence_graph() (in module NORDic.UTILS.utils_plot) plot_precision_recall() (in module NORDic.UTILS.utils_plot)

plot_roc_curve() (in module NORDic.UTILS.utils_plot) plot_signatures() (in module NORDic.UTILS.utils_plot) post_request() (in module NORDic.UTILS.LINCS_utils) profiles2signatures() (in module NORDic.UTILS.utils_exp) projection() (in module NORDic.NORDic_DR.utils) pubchem2drugname() (in module NORDic.NORDic_DS.get_drug_signatures)

Q

quadprog_solve_qp() (in module NORDic.NORDic_DR.utils)

quantile_normalize() (in module NORDic.UTILS.utils_state)

R

randf() (in module NORDic.NORDic_DR.utils) reconnect_network() (in module NORDic.UTILS.utils_grn) remove_isolated() (in module NORDic.UTILS.utils_network) request_biodbnet() (in module NORDic.UTILS.utils_data)

retrieve_drug_signature() (in module NORDic.NORDic_DS.get_drug_signatures) retrieve_drug_targets() (in module NORDic.NORDic_DS.get_drug_targets) reward() (NORDic.NORDic_DR.functions.testing_problem method) run() (NORDic.NORDic_DR.bandits.Misspecified method) run_experiments() (in module NORDic.NORDic_PMR.functions)

S

sample() (NORDic.NORDic_DR.bandits.Misspecified method) save_grn() (in module NORDic.UTILS.utils_grn) save_solutions() (in module NORDic.UTILS.utils_grn) select_best_sig() (in module NORDic.UTILS.LINCS_utils) select_optimal_model() (in module NORDic.NORDic_NI.functions) sherman_morrison() (in module NORDic.NORDic_DR.utils) simulate() (in module NORDic.NORDic_DS.functions) simulate_treatment() (in module NORDic.NORDic_DS.functions) solution2cytoscape() (in module NORDic.NORDic_NI.functions)

solution2influences() (in module NORDic.UTILS.utils_grn) solution_generation() (in module NORDic.NORDic_NI.functions) solve_alternative_quadprog() (in module NORDic.NORDic_DR.utils) spread() (in module NORDic.NORDic_PMR.functions) spread_multistate() (in module NORDic.NORDic_PMR.functions) stopping_rule() (NORDic.NORDic_DR.bandits.LinGapE method) (NORDic.NORDic_DR.bandits.MisLid method) string_api_url() (in module NORDic.UTILS.STRING_utils) subheuristic() (in module NORDic.NORDic_DR.bandits)

T

test() (in module NORDic.UTILS.utils_sim)

testing_problem (class in NORDic.NORDic_DR.functions) tracking_rule() (in module NORDic.NORDic_DR.utils)

U

up_to_attractors() (NORDic.UTILS.utils_sim.BN_SIM method) update() (NORDic.NORDic_DR.bandits.LinGapE method) (NORDic.NORDic_DR.bandits.MisLid method)

update_misspecified() (in module NORDic.NORDic_DR.utils) update_network() (NORDic.UTILS.utils_sim.BN_SIM method)

V

visualize_models() (in module NORDic.NORDic_NI.functions)

Z

zip2df() (in module NORDic.UTILS.utils_grn)