NORDic

• NORDic NI module
  • NORDic.NORDic_NI.functions module
    • import_all_solutions()
    • network_identification()
    • select_optimal_model()
    • solution2cytoscape()
    • solution_generation()
    • visualize_models()
• NORDic PMR module
  • NORDic.NORDic_PMR.functions module
    • compute_similarities()
    • greedy()
    • run_experiments()
    • spread()
    • spread_multistate()
• NORDic DS module
  • NORDic.NORDic_DS.functions module
    • baseline()
    • compute_frontier()
    • compute_metrics()
    • compute_score()
    • empirical_pvalue()
    • simulate()
    • simulate_treatment()
  • NORDic.NORDic_DS.get_drug_signatures module
    • compute_drug_signatures_L1000()
    • drugname2pubchem()
    • get_ranking()
    • pubchem2drugname()
    • retrieve_drug_signature()
  • NORDic.NORDic_DS.get_drug_targets module
    • get_targets_DrugBank()
    • get_targets_DrugCentral()
    • get_targets_LINCS()
    • get_targets_MINERVA()
    • get_targets_TTD()
    • retrieve_drug_targets()
• NORDic DR module
  • NORDic.NORDic_DR.bandits module
    • AdaHedge
      • AdaHedge.act()
      • AdaHedge.incur()
    • Greedy
      • Greedy.act()
      • Greedy.incur()
    • Learner
      • Learner.act()
      • Learner.incur()
    • LinGapE
      • LinGapE.apply()
      • LinGapE.greedy()
      • LinGapE.optimized()
      • LinGapE.stopping_rule()
      • LinGapE.update()
    • MisLid
      • MisLid.apply()
      • MisLid.best_answer()
      • MisLid.stopping_rule()
      • MisLid.update()
    • Misspecified
      • Misspecified.clear()
      • Misspecified.run()
      • Misspecified.sample()
    • gaussian()
    • heuristic()
    • misspecified()
    • subheuristic()
  • NORDic.NORDic_DR.functions module
    • adaptive_testing()
    • testing_problem
      • testing_problem.reward()
  • NORDic.NORDic_DR.utils module
    • argmax_m()
    • barycentric_spanner()
    • c_kt()
    • closest_alternative()
    • cnorm()
    • lambert()
    • mahalanobis()
    • optimistic_gradient()
    • projection()
    • quadprog_solve_qp()
    • randf()
    • sherman_morrison()
    • solve_alternative_quadprog()
    • tracking_rule()
    • update_misspecified()
• NORDic UTILS module
  • NORDic.UTILS.DISGENET_utils module
    • get_genes_evidences_from_DISGENET()
    • get_genes_proteins_from_DISGENET()
    • get_user_key_DISGENET()
  • NORDic.UTILS.LINCS_utils module
    • binarize_via_CD()
    • build_url()
    • compute_interference_scale()
    • convert_ctrlgenes_EntrezGene()
    • create_restricted_drug_signatures()
    • download_file()
    • download_lincs_files()
    • get_treated_control_dataset()
    • get_user_key()
    • post_request()
    • select_best_sig()
  • NORDic.UTILS.STRING_utils module
    • get_app_name_STRING()
    • get_image_from_STRING()
    • get_interactions_from_STRING()
    • get_interactions_partners_from_STRING()
    • get_network_from_STRING()
    • get_protein_names_from_STRING()
    • string_api_url()
  • NORDic.UTILS.utils_data module
    • convert_EntrezGene_LINCSL1000()
    • convert_genes_EntrezGene()
    • get_all_celllines()
    • request_biodbnet()
  • NORDic.UTILS.utils_exp module
    • get_experimental_constraints()
    • profiles2signatures()
  • NORDic.UTILS.utils_grn module
    • CL()
    • Centr()
    • DS()
    • GT()
    • build_influences()
    • build_observations()
    • create_grn()
    • desirability()
    • general_topological_parameter()
    • get_genes_downstream()
    • get_genes_interactions_from_PPI()
    • get_genes_most_variable()
    • get_grfs_from_solution()
    • get_maxdegree()
    • get_minimal_edges()
    • get_weakly_connected()
    • infer_network()
    • load_grn()
    • reconnect_network()
    • save_grn()
    • save_solutions()
    • solution2influences()
    • zip2df()
  • NORDic.UTILS.utils_network module
    • aggregate_networks()
    • capture()
    • determine_edge_threshold()
    • get_network_from_OmniPath()
    • merge_network_PPI()
    • remove_isolated()
  • NORDic.UTILS.utils_plot module
    • influences2graph()
    • plot_boxplots()
    • plot_discrete_distributions()
    • plot_distributions()
    • plot_heatmap()
    • plot_influence_graph()
    • plot_precision_recall()
    • plot_roc_curve()
    • plot_signatures()
  • NORDic.UTILS.utils_sim module
    • BN_SIM
      • BN_SIM.add_initial_states()
      • BN_SIM.add_permanent_mutation()
      • BN_SIM.add_transient_mutation()
      • BN_SIM.attrs_similarity()
      • BN_SIM.boxplot()
      • BN_SIM.enumerate_attractors()
      • BN_SIM.generate_trajectories()
      • BN_SIM.initialize_network()
      • BN_SIM.up_to_attractors()
      • BN_SIM.update_network()
    • BONESIS_SIM
      • BONESIS_SIM.add_initial_states()
      • BONESIS_SIM.add_permanent_mutation()
      • BONESIS_SIM.add_transient_mutation()
      • BONESIS_SIM.enumerate_attractors()
      • BONESIS_SIM.generate_trajectories()
      • BONESIS_SIM.initialize_network()
    • MABOSS_SIM
      • MABOSS_SIM.add_initial_states()
      • MABOSS_SIM.add_permanent_mutation()
      • MABOSS_SIM.add_transient_mutation()
      • MABOSS_SIM.enumerate_attractors()
      • MABOSS_SIM.generate_trajectories()
      • MABOSS_SIM.initialize_network()
    • MPBN_SIM
      • MPBN_SIM.add_initial_states()
      • MPBN_SIM.add_permanent_mutation()
      • MPBN_SIM.add_transient_mutation()
      • MPBN_SIM.enumerate_attractors()
      • MPBN_SIM.generate_trajectories()
      • MPBN_SIM.initialize_network()
    • capture()
    • choice()
    • test()
  • NORDic.UTILS.utils_state module
    • binarize_experiments()
    • compare_states()
    • finetune_binthres()
    • quantile_normalize()