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 (FN)
calculate_models_synergies_fp
                        Count the predictions of the non-synergistic
                        drug combinations per model (FP)
calculate_models_synergies_tn
                        Count the non-synergies of the non-synergistic
                        drug combinations per model (TN)
calculate_models_synergies_tp
                        Count the predictions of the observed synergies
                        per model (TP)
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 prediction
get_avg_activity_diff_based_on_synergy_set_cmp
                        Get the average activity difference based on
                        the comparison of two synergy sets
get_avg_activity_diff_based_on_tp_predictions
                        Get the average activity difference based on
                        the number of true positives
get_avg_activity_diff_mat_based_on_mcc_clustering
                        Get average activity difference matrix based on
                        MCC clustering
get_avg_activity_diff_mat_based_on_specific_synergy_prediction
                        Get average activity difference matrix based on
                        specific synergy prediction
get_avg_activity_diff_mat_based_on_tp_predictions
                        Get average activity difference matrix based on
                        the number of true positives
get_avg_link_operator_diff_based_on_synergy_set_cmp
                        Get the average link operator difference based
                        on the comparison of two synergy sets
get_avg_link_operator_diff_mat_based_on_mcc_clustering
                        Get average link operator difference matrix
                        based on MCC clustering
get_avg_link_operator_diff_mat_based_on_specific_synergy_prediction
                        Get average link operator difference matrix
                        based on specific synergy prediction
get_avg_link_operator_diff_mat_based_on_tp_predictions
                        Get average link operator difference matrix
                        based on the number of true positives
get_biomarkers          Get total biomarkers from average data
                        differences matrix
get_biomarkers_per_type
                        Get biomarkers from average data differences
                        matrix (per type)
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 synergies
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 matrix
plot_avg_state_diff_graph
                        Plot the graph of average state differences
                        (igraph)
plot_avg_state_diff_graph_vis
                        Plot the graph of average state differences
                        (visNetwork)
plot_avg_state_diff_graphs
                        Plot the graphs from an average state
                        differences matrix
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
