Package: MetaPathNet 0.99.1

Zhaojie Wang

MetaPathNet: KEGG-Based Metabolic and Signaling Network Analysis for Systems Biology

Provides tools to construct KEGG-based metabolic and signaling networks as edge lists for single-organism or cross-species analyses. The package supports identifier mapping, shortest-path and topology analyses, community detection, permutation testing, pathway over-representation analysis, and node annotation for host-microbiome studies. It also provides network visualisation in R and Cytoscape and supports extension of KEGG-based networks through additional reaction resources and user-defined reactions.

Authors:Zhaojie Wang [aut, cre], Francesc Puig-Castellvi [aut], Manyi Jia [aut], Marc-Emmanuel Dumas [aut, ths]

MetaPathNet_0.99.1.tar.gz
MetaPathNet_0.99.1.zip(r-4.7)MetaPathNet_0.99.1.zip(r-4.6)MetaPathNet_0.99.1.zip(r-4.5)
MetaPathNet_0.99.1.tgz(r-4.6-any)MetaPathNet_0.99.1.tgz(r-4.5-any)
MetaPathNet_0.99.1.tar.gz(r-4.7-any)MetaPathNet_0.99.1.tar.gz(r-4.6-any)
MetaPathNet_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MetaPathNet/json (API)
NEWS

# Install 'MetaPathNet' in R:
install.packages('MetaPathNet', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zhaojie-wang/metapathnet/issues

Datasets:

On CRAN:

Conda:

networkpathwayskeggsystemsbiologyclassificationmicrobiome

2.30 score 26 exports 166 dependencies

Last updated from:e932e76d01. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE205
linux-devel-x86_64OK467
source / vignettesOK436
linux-release-x86_64OK468
macos-release-arm64OK405
macos-oldrel-arm64OK343
windows-develOK424
windows-releaseOK461
windows-oldrelOK426
wasm-releaseOK193

Exports:MPN_annotateKoClassMPN_annotateOriginMPN_clusterNetworkMPN_compoundEgoNetworkMPN_convertGeneMPN_crossSpeciesNetworkMPN_customReactionMPN_distancesMPN_egoNetworkMPN_enrichPathwayMPN_findMappedNodesMPN_getPathIDsMPN_keggFinderMPN_keggNetworkMPN_mapReactionMPN_mergeNetworksMPN_netSimilarityMPN_permutePathsMPN_removeDrugsMPN_removeNodeMPN_replaceNodeMPN_shortestPathsMPN_suggestEntitiesMPN_viewClusterCyMPN_viewNetworkCyMPN_viewNetworkR

Dependencies:abindAnnotationDbiaskpassbackportsbase64encbase64urlBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcaToolscheckmatechroncigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tabledata.treeDBIdbplyrDelayedArraydigestdplyrevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggplot2ggraphggrepelgluegplotsgraphgraphlayoutsgridExtragsubfngtablegtoolshighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphIRangesIRdisplayIRkernelisobandjquerylibjsonliteKEGGgraphKEGGRESTKernSmoothknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemygenennetopensslpbdZMQpillarpkgconfigplyrpngpolyclipprettyunitsprogressprotopurrrR6rappdirsRColorBrewerRcppRcppArmadilloRCurlRCy3reprrestfulrRgraphvizRhtslibrjsonRJSONIOrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerrvestS4ArraysS4VectorsS7sassscalesselectrSeqinfosnowSparseArraysqldfstringistringrSummarizedExperimentsyssystemfontstibbletidygraphtidyrtidyselecttinytextweenrtxdbmakerUCSC.utilsutf8uuidvctrsviridisviridisLitewebchemwithrxfunXMLxml2XVectoryaml

MetaPathNet: network analysis of the choline-TMA-TMAO host-microbiome axis

Zhaojie WangFrancesc Puig-CastellvĂ­Marc-Emmanuel Dumas

Rendered fromMetaPathNet-choline-TMA-TMAO.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2026-04-30
Started: 2026-04-30

Readme and manuals

Help Manual

Help pageTopics
Example tryptophan-related MetaPathNet networkMetaPathNet_example_network
Annotate KO functional class (metabolic vs signalling)MPN_annotateKoClass
Annotate KO Origin (Host vs Bacteria) and Optionally Export to CytoscapeMPN_annotateOrigin
Community Detection in KEGG-Derived NetworksMPN_clusterNetwork
Build compound-centred ego subnetworks across KEGG organismsMPN_compoundEgoNetwork
Convert Ensembl or Entrez Gene IDs to KEGG Gene IDs and KO TermsMPN_convertGene
Build Cross-Species MetaPathNet NetworkMPN_crossSpeciesNetwork
Build MetaPathNet-style edges from user-defined reactionsMPN_customReaction
Calculate Shortest-Path Distances Between Node Sets in a KEGG-Based NetworkMPN_distances
Extract an Ego Subnetwork from a Metabolic / Signalling NetworkMPN_egoNetwork
Pathway Enrichment Analysis (Over-representation Analysis) on KEGG-Based Node SetsMPN_enrichPathway
Map User-Supplied Nodes to a NetworkMPN_findMappedNodes
Retrieve and Classify Organism-Specific KEGG PathwaysMPN_getPathIDs
Find KEGG Identifiers for Compounds, Organisms, and KO TermsMPN_keggFinder
Build KEGG Metabolic and Signaling NetworkMPN_keggNetwork
Map reaction IDs to MetaPathNet-style networksMPN_mapReaction
Merge Multiple MetaPathNet-Style NetworksMPN_mergeNetworks
Compare KEGG-Based Networks via Jaccard SimilarityMPN_netSimilarity
Permutation Test of Shortest-Path Structure Between Node SetsMPN_permutePaths
Remove Drug Nodes from a Network MatrixMPN_removeDrugs
Remove Specified Nodes from a Network MatrixMPN_removeNode
Replace Nodes in a Network TableMPN_replaceNode
Identify Shortest Paths Between Node Sets in a KEGG-Derived NetworkMPN_shortestPaths
Suggest Candidate Organisms or KOs from KEGG IdentifiersMPN_suggestEntities
Visualise Clustered MetaPathNet Networks in CytoscapeMPN_viewClusterCy
Visualize a KEGG-Derived Network in Cytoscape via RCy3MPN_viewNetworkCy
Visualise a KEGG-Based Network Matrix in RMPN_viewNetworkR