Ensemble Boolean Model Biomarker Analysis

add_numbers_above_the_bars | Add numbers horizontally above the bars of a barplot |

assign_link_operator_value_to_equation | Assign link operator value to boolean equation |

biomarker_mcc_analysis | Biomarker analysis based on MCC model classification |

biomarker_synergy_analysis | Biomarker analysis per synergy predicted |

biomarker_tp_analysis | Biomarker analysis based on TP model classification |

calculate_mcc | Calculate Matthews correlation coefficient vector |

calculate_models_mcc | Calculate the Matthews correlation coefficient for each model |

calculate_models_synergies_fn | Count the non-synergies of the observed synergies per model... |

calculate_models_synergies_fp | Count the predictions of the non-synergistic drug... |

calculate_models_synergies_tn | Count the non-synergies of the non-synergistic drug... |

calculate_models_synergies_tp | Count the predictions of the observed synergies per model... |

construct_network | Construct igraph network graph |

count_models_that_predict_synergies | Count models that predict a set of synergies |

emba | emba |

filter_network | Filter the network's vertices |

get_alt_drugname | Get alternative drug combination name |

get_avg_activity_diff_based_on_mcc_clustering | Get the average activity difference based on MCC clustering |

get_avg_activity_diff_based_on_specific_synergy_prediction | Get average activity difference based on specific synergy... |

get_avg_activity_diff_based_on_synergy_set_cmp | Get the average activity difference based on the comparison... |

get_avg_activity_diff_based_on_tp_predictions | Get the average activity difference based on the number of... |

get_avg_activity_diff_mat_based_on_mcc_clustering | Get average activity difference matrix based on MCC... |

get_avg_activity_diff_mat_based_on_specific_synergy_prediction | Get average activity difference matrix based on specific... |

get_avg_activity_diff_mat_based_on_tp_predictions | Get average activity difference matrix based on the number of... |

get_avg_link_operator_diff_based_on_synergy_set_cmp | Get the average link operator difference based on the... |

get_avg_link_operator_diff_mat_based_on_mcc_clustering | Get average link operator difference matrix based on MCC... |

get_avg_link_operator_diff_mat_based_on_specific_synergy_prediction | Get average link operator difference matrix based on specific... |

get_avg_link_operator_diff_mat_based_on_tp_predictions | Get average link operator difference matrix based on the... |

get_biomarkers | Get total biomarkers from average data differences matrix |

get_biomarkers_per_type | Get biomarkers from average data differences matrix (per... |

get_edges_from_topology_file | Get the edges from a specified topology |

get_fitness_from_models_dir | Load the models fitness scores |

get_link_operators_from_models_dir | Load the models boolean equation link operator data |

get_model_names | Get the model names |

get_model_predictions | Load the models predictions data |

get_models_based_on_mcc_class_id | Get models based on the MCC class id |

get_neighbors | Get neighbor nodes |

get_node_colors | Get the node colors |

get_node_names | Get the node names |

get_observed_model_predictions | Subset the model predictions to the (true) observed synergies |

get_observed_synergies | Load the observed synergies data |

get_observed_synergies_per_cell_line | Get observed synergies per cell line |

get_perf_biomarkers_per_cell_line | Get performance biomarkers per cell line |

get_stable_state_from_models_dir | Load the models stable state data |

get_synergy_biomarkers_from_dir | Get synergy biomarkers from dir |

get_synergy_biomarkers_per_cell_line | Get synergy biomarkers per cell line |

get_synergy_comparison_sets | Get synergy comparison sets |

get_synergy_scores | Get synergy scores from file |

get_synergy_subset_stats | Find the number of predictive models for every synergy subset |

get_unobserved_model_predictions | Subset the model predictions to the (false) non-observed... |

get_vector_diff | Calculate difference vector with penalty term |

get_x_axis_values | Get the refined x-axis values |

is_comb_element_of | Is drug combination element of given vector? |

make_barplot_on_models_stats | Bar plot of model stats |

make_barplot_on_synergy_subset_stats | Bar plot of observed synergy subsets |

plot_avg_link_operator_diff_graph | Plot the graph of average link operator differences (igraph) |

plot_avg_link_operator_diff_graphs | Plot the graphs from an average link operator differences... |

plot_avg_state_diff_graph | Plot the graph of average state differences (igraph) |

plot_avg_state_diff_graphs | Plot the graphs from an average state differences matrix |

plot_avg_state_diff_graph_vis | Plot the graph of average state differences (visNetwork) |

plot_mcc_classes_hist | Plot histogram of the MCC classes |

print_biomarkers_per_predicted_synergy | Print biomarkers for each predicted synergy |

print_model_and_drug_stats | Print model and drug statistics |

update_biomarker_files | Update biomarker files for a specific synergy |

validate_observed_synergies_data | Validate observed synergies data |

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