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Introduction

  • Introduction
    • Introduction to dingo
    • Introduction to dingo-stats
  • Installation
    • Installation of dingo
    • Installation of dingo-stats
    • How to build the ReadTheDocs of dingo-stats locally

Tutorials

  • Getting started
    • Load and Modify models
    • Perform Sampling
    • Inspect Sampling distributions
  • KEGG pathways information
    • Map model reactions IDs to KEGG terms
    • Subset reactions from pathways
  • Reduce thermodynamic infeasible samples
    • Identify and remove loopy reactions
    • Quantify the effect of loopy reactions in sampling
  • Differential Flux Analysis
    • Compare reaction flux distributions across conditions with a Kolmogorov–Smirnov test
    • Hypergeometric test for pathway enrichment
  • Correlations from reactions samples
    • Prerequisites for calculating pairwise correlations
    • Calculation of pairwise linear correlations and non-linear copula dependencies
  • Clustering from correlation matrix
    • Prerequisites for annotating the produced dendrogram
    • Hierarchical Clustering with Dendrogram Visualization
    • Benchmarking with other clustering methods
  • Graphs from correlation matrix
    • Prerequisites for annotating the produced graph
    • Construct a graph
    • Visualize the constructed graph

API

  • API Reference
    • gapsplit
      • Attributes
      • Functions
      • Module Contents
        • gapsplit()
        • _generate_sample()
        • _generate_sample_gurobi_direct()
        • _maxgap()
        • _make_report_header()
        • _reduce_gurobi()
        • model
    • graphs_utils
      • Functions
      • Module Contents
        • construct_graph()
        • draw_positive_clique_shadows()
        • draw_negative_clique_shadows()
        • plot_graph()
        • compute_nodes_centrality_metrics()
        • compare_essential_to_network_central_reactions()
        • compare_network_modularities()
        • compare_node_centralities()
    • loopless_utils
      • Functions
      • Module Contents
        • loops_enumeration_from_fva()
        • loopy_reactions_turned_off_in_pfba()
        • get_loopless_solutions_from_samples()
        • calculate_affected_samples()
        • calculate_distances_from_samples()
        • calculate_distances_from_reactions()
        • violin_plot_samples_distances()
    • pathways_utils
      • Functions
      • Module Contents
        • read_json_file()
        • map_model_to_kegg_reactions_dictionary()
        • dictionary_reaction_id_to_kegg_id()
        • reaction_id_to_kegg_id()
        • fill_missing_kegg_ids_in_initial_dictionary()
        • fetch_kegg_pathway()
        • get_kegg_pathways_from_reaction_ids()
        • subset_model_reactions_from_pathway_info()
        • dictionary_reaction_id_to_pathway()
        • reaction_in_pathway_binary_matrix()
        • plot_reaction_in_pathway_heatmap()
        • sort_reactions_by_model_order()
        • subset_sampling_array_from_reaction_ids()
        • dictionary_map_reverse_reaction_id_to_pathway()
    • clustering_utils
      • Functions
      • Module Contents
        • clustering_of_correlation_matrix()
        • plot_dendrogram()
    • escher_maps_utils
      • Attributes
      • Functions
      • Module Contents
        • BIGG_COFACTORS
        • BIGG_BUILDING_BLOCLS
        • MODELSEED_COFACTORS
        • EXCLUDED_COMPOUNDS
        • remove_cycles()
        • build_reaction_hierarchy()
        • build_escher_map()
    • correlations_utils
      • Attributes
      • Functions
      • Module Contents
        • BIGG_COFACTORS
        • BIGG_BUILDING_BLOCKS
        • MODELSEED_COFACTORS
        • correlated_reactions()
        • plot_correlation_matrix()
        • compute_copula()
        • copula_tail_dependence()
        • plot_copula()
        • split_forward_reverse()
        • find_reactants_products()
        • sharing_metabolites()
        • sharing_metabolites_square_matrix()
    • load_modify_sample_utils
      • Functions
      • Module Contents
        • load_model()
        • get_objective_functions()
        • get_reaction_bounds()
        • modify_model()
        • sample_optgp()
        • sample_dingo()
        • sample_gapsplit()
        • export_to_pickle()
        • load_from_pickle()
        • plot_grid_reactions_flux()
        • sampling_statistics()
    • distributions_comparison_utils
      • Functions
      • Module Contents
        • significantly_altered_reactions()
        • plot_volcano()
        • dictionary_reaction_to_all_pathways()
        • hypergeometric_test_pathway_enrichment()
        • plot_pathway_enrichment()
dingo-stats
  • API Reference
  • View page source

API Reference

This page contains auto-generated API reference documentation [1].

  • gapsplit
  • graphs_utils
  • loopless_utils
  • pathways_utils
  • clustering_utils
  • escher_maps_utils
  • correlations_utils
  • load_modify_sample_utils
  • distributions_comparison_utils
[1]

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