KEGG-Based Metabolic and Signaling Network Analysis for Systems Biology

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Documentation for package ‘MetaPathNet’ version 0.99.5

Help Pages

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
enrichmentDotPlot Create a Dot Plot of Pathway Enrichment Results
enrichPathway Pathway Enrichment Analysis on KEGG-Based Node Sets
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
MetaPathNet_example_network Example tryptophan-related MetaPathNet network
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