Welcome to NORDic’s documentation!

Being able to build in an automated and reproducible way a model of gene interactions and their influences on gene activity will allow to consider more complex diseases and biological phenomena, on a larger set of genes. These models might speed up the understanding of the gene regulation hierarchy by bioinformaticians and biologists, allow to predict novel drugs or gene targets which might be investigated later for healthcare purposes. In particular, the network-oriented approach allow to predict off-targets, which are non-specific drug targets which might lead to otherwise unexpected toxic side effects.

NORDic is an open-source package which allows to focus on a network-oriented approach to identify regulatory mechanisms linked to a disease, to detect master regulators in a diseased transcriptomic context, to simulate drug effects on a patient through a network, and adaptively test drugs to perform sample-efficient, error-bound drug repurposing.

• Introduction to NORDic
  • Statement of need
  • Automated identification of disease-related Boolean networks (NORDic NI)
  • Prioritization of master regulators in Boolean networks (NORDic PMR)
  • Novel approaches for scoring drug effects & repurposing drugs (NORDic DS & DR)
  • Extraction of information from large public data sets & simulation module (NORDic UTILS)
  • Summary
• Installation
  • Supported platforms
  • Dependencies
  • Using pip (package hosted on PyPI)
  • Using conda (package hosted on Anaconda.org)
  • Using CoLoMoTo-Docker (since March 1st, 2023)
  • From Source Files
• Statement of need
• Usage
  • Quick access to NORDic
  • Environment
  • Example usage
• 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
      • Greedy
      • Learner
      • LinGapE
      • MisLid
      • Misspecified
      • gaussian()
      • heuristic()
      • misspecified()
      • subheuristic()
    • NORDic.NORDic_DR.functions module
      • adaptive_testing()
      • testing_problem
    • 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
      • BONESIS_SIM
      • MABOSS_SIM
      • MPBN_SIM
      • capture()
      • choice()
      • test()
    • NORDic.UTILS.utils_state module
      • binarize_experiments()
      • compare_states()
      • finetune_binthres()
      • quantile_normalize()

Indices and tables

• Index

• Module Index