calculate_interaction_score
                        Calls a python script to calculate interaction
                        score for combined graphs
check_connection        Checks connection
check_drug_target       Check drug target interaction data
check_drug_targets_in_layers
                        Check drug target and layer data
check_input             Check pipeline input data for required format
check_layer             Check layer input
check_sensible_connections
                        Check connection and layer data
chunk                   Create chunks from a vector for parallel
                        computing
chunk_2gether           Create chunks from two vectors for parallel
                        computing
combine_graphs          Combining graphs by adding inter-layer edges
combined_graphs_example
                        Combined graphs
corPvalueStudentParallel
                        Compute p-values for upper triangle of
                        correlation matrix in parallel
create_unique_layer_node_ids
                        Assigns node IDs to the biological identifiers
                        across a graph layer
determine_drug_targets
                        Determine drug target nodes in network
differential_score      The absolute difference of interaction score of
                        two groups
differential_score_graph_example
                        Differential graph
drug_gene_interactions
                        Drug-gene interactions
drug_response_score_example
                        Drug response score
drug_target_interaction_example
                        Drug target interaction example data
drug_targets_example    Drug target nodes in combined network
find_targets            Filter drug target nodes
generate_combined_graphs
                        Combines individual layers to a single graph
generate_individual_graphs
                        Builds graphs from specified network layers
generate_reduced_graph
                        Generate a reduced iGraph
get_drug_response_score
                        Calculate drug response score
get_layer               [INTERNAL] Fetch layer by name from layer
                        object
get_layer_setting       Get layer settings
graph_metrics           Analyses metrics of an iGraph object
individual_graphs_example
                        Individual graphs
install_python_dependencies
                        Installs python dependencies needed for
                        interaction score computation
inter_layer_edgelist_by_id
                        Interlayer conntections by identifiers
inter_layer_edgelist_by_table
                        Interaction table to iGraph graph object
interaction_score       Computes interaction score for combined graphs
interaction_score_graphs_example
                        Interaction score graphs
interaction_score_graphs_vignette
                        Interaction score graphs for vignette
layers_example          Formatted layers object
load_interaction_score_output
                        Loads output of python script for interaction
                        score calculation
make_connection         Specify connection between two individual
                        layers
make_drug_target        Reformat drug-target-interaction data
make_layer              Creates individual molecular layers from raw
                        data and unique identifiers
metabolite_data         Metabolomics data
metabolite_protein_interaction
                        Metabolite protein interaction data
molnet_settings         Create global settings variable for molnet
                        pipeline
mrna_data               mRNA expression data
network_reduction_by_p_value
                        Reduce the the entries in an adjacency matrix
                        by thresholding on p-values
network_reduction_by_pickHardThreshold
                        Reduces network based on
                        WGCNA::pickHardThreshold function
phosphoprotein_data     Phosphosite data
pickHardThreshold_alternative
                        Alternative implementation of
                        WGCNA::pickHardThreshold
protein_data            Protein data
return_errors           Return detected errors
sample_size             Sample size for correlation computation
scaleFreeFitIndex_alternative
                        Alternative implementation of
                        WGCNA::scaleFreeFitIndex
set_cluster             Create and register cluster
shutdown_cluster        Shutdown cluster and remove corresponding
                        connections
start_pipeline          Execute all molnet-pipeline steps sequentially
target_edge_list        Edges adjacent to target nodes
write_interaction_score_input
                        Write edge lists and combined graphs to files
