Compartment and Hub Definitions Tune Metabolic Networks for Metabolomic Interpretations

This archive contains data for a report by the same title. Data relate to software projects MetaboNet and DyMetaboNet. MetaboNet: https://github.com/tcameronwaller/metabonet DyMetaboNet: https://github.com/tcameronwaller/dymetabonet File descriptions dymetabonet_2019-08-29.mp4 ... raw screen capture video of DyMetaboNet dock_metabonet_2019-08-18.zip ... complete MetaboNet export model_* ... curation of human metabolic model by MetaboNet model_dymetabonet.zip ... format for DyMetaboNet model_compartments* ... compartments model_processes* ... processes model_reactions* ... reactions model_metabolites* ... metabolites measurement_* ... curation of metabolomic measurements by MetaboNet measurement_study_*_report.tsv ... summary of match measurements to metabolites measurement_study_*.tsv ... metabolites' fold changes and probabilities between groups measurement_study_*_metaboanalyst.txt ... format for MetaboAnalyst measurement_study_*_metaboanalyst_pair.txt ... format for MetaboAnalyst with sample pairs network_* ... multiple definitions of metabolic networks network_compartments-true_hubs-true.zip ... compartmental network with hubs network_compartments-true_hubs-false.zip ... compartmental network without hubs network_compartments-false_hubs-true.zip ... noncompartmental network with hubs network_compartments-false_hubs-false.zip ... noncompartmental network without hubs network_compartments-*_hubs_*/network_cytoscape.json ... format for Cytoscape network_compartments-*_hubs_*/network_networkx.pickle ... format for NetworkX network_compartments-*_hubs_*/nodes_reactions.pickle ... network's nodes for reactions network_compartments-*_hubs_*/nodes_metabolites.pickle ... network's nodes for metabolites network_compartments-*_hubs_*/links.pickle ... network's links network_compartments-*_hubs_*/analysis/nodes_reactions.tsv ... nodes' metrics relative to reactions network_compartments-*_hubs_*/analysis/nodes_metabolites.tsv ... nodes' metrics relative to metabolites network_compartments-*_hubs_*/analysis/network_reactions.tsv ... network's metrics relative to reactions network_compartments-*_hubs_*/analysis/network_metabolites.tsv ... network's metrics relative to metabolites network_compartments-*_hubs_*/measurement/metabolites.tsv ... measurements on nodes for metabolites