| calculate_interaction_score | Calls a python script to calculate interaction score for... |
| 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 |
| combined_graphs_example | Combined graphs |
| combine_graphs | Combining graphs by adding inter-layer edges |
| corPvalueStudentParallel | Compute p-values for upper triangle of correlation matrix in... |
| create_unique_layer_node_ids | Assigns node IDs to the biological identifiers across a graph... |
| 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... |
| interaction_score | Computes interaction score for combined graphs |
| interaction_score_graphs_example | Interaction score graphs |
| interaction_score_graphs_vignette | Interaction score graphs for vignette |
| inter_layer_edgelist_by_id | Interlayer conntections by identifiers |
| inter_layer_edgelist_by_table | Interaction table to iGraph graph object |
| layers_example | Formatted layers object |
| load_interaction_score_output | Loads output of python script for interaction score... |
| 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... |
| 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_pickHardThreshold | Reduces network based on WGCNA::pickHardThreshold function |
| network_reduction_by_p_value | Reduce the the entries in an adjacency matrix by thresholding... |
| phosphoprotein_data | Phosphosite data |
| pickHardThreshold_alternative | Alternative implementation of WGCNA::pickHardThreshold |
| pipe | Pipe operator |
| 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 |
