MetaPathNet_example_network
                        Example tryptophan-related MetaPathNet network
addCustomReaction       Build MetaPathNet-style edges from user-defined
                        reactions
annotateKoClass         Annotate KO functional class (metabolic vs
                        signalling)
annotateOrigin          Annotate KO Origin (Host vs Bacteria) and
                        Optionally Export to Cytoscape
buildCompoundEgoNetwork
                        Build compound-centred ego subnetworks across
                        KEGG organisms
buildCrossSpeciesNetwork
                        Build Cross-Species MetaPathNet Network
buildEgoNetwork         Extract an Ego Subnetwork from a Metabolic /
                        Signalling Network
buildKeggNetwork        Build KEGG Metabolic and Signaling Network
clusterNetwork          Community Detection in KEGG-Derived Networks
combineNetworks         Merge Multiple MetaPathNet-Style Networks
convertGene             Convert Ensembl or Entrez Gene IDs to KEGG Gene
                        IDs and KO Terms
enrichPathway           Pathway Enrichment Analysis on KEGG-Based Node
                        Sets
enrichmentDotPlot       Create a Dot Plot of Pathway Enrichment Results
findKeggIDs             Find KEGG Identifiers for Compounds, Organisms,
                        and KO Terms
findMappedNodes         Map User-Supplied Nodes to a Network
findShortestPaths       Identify Shortest Paths Between Node Sets in a
                        KEGG-Derived Network
getPathIDs              Retrieve and Classify Organism-Specific KEGG
                        Pathways
mapReaction             Map reaction IDs to MetaPathNet-style networks
networkDistances        Calculate Shortest-Path Distances Between Node
                        Sets in a KEGG-Based Network
networkSimilarity       Compare KEGG-Based Networks via Jaccard
                        Similarity
permutePaths            Permutation Test of Shortest-Path Structure
                        Between Node Sets
removeDrugs             Remove Drug Nodes from a Network Matrix
removeNetworkNodes      Remove Specified Nodes from a Network Matrix
replaceNode             Replace Nodes in a Network Table
suggestEntities         Suggest Candidate Prokaryotic Organisms or KOs
                        from KEGG Identifiers
viewClusterCy           Visualise Clustered MetaPathNet Networks in
                        Cytoscape
viewNetworkCy           Visualize a KEGG-Derived Network in Cytoscape
                        via RCy3
viewNetworkR            Visualise a KEGG-Based Network Matrix in R
