Package: MetaPathNet 0.99.5

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], Centre National de la Recherche Scientifique [fnd], Imperial College London [fnd], French National Research Agency [fnd]

MetaPathNet_0.99.5.tar.gz
MetaPathNet_0.99.5.zip(r-4.7-any)MetaPathNet_0.99.5.zip(r-4.6-any)MetaPathNet_0.99.5.zip(r-4.5-any)
MetaPathNet_0.99.5.tgz(r-4.6-any)MetaPathNet_0.99.5.tgz(r-4.5-any)
MetaPathNet_0.99.5.tar.gz(r-4.7-any)MetaPathNet_0.99.5.tar.gz(r-4.6-any)
MetaPathNet_0.99.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MetaPathNet/json (API)

# Install 'MetaPathNet' in R:

install.packages('MetaPathNet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

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

Datasets:

MetaPathNet_example_network - Example tryptophan-related MetaPathNet network

On BioConductor:MetaPathNet-0.99.5(bioc 3.24)

network pathways kegg systemsbiology classification microbiome

3.90 score 2 stars 596 downloads 27 exports 160 dependencies

Last updated from:fdaae4de76. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	184
linux-devel	OK	430
source / vignettes	OK	357
linux-release	OK	417
macos-release	OK	275
macos-oldrel	OK	237
windows-devel	OK	315
windows-release	OK	302
windows-oldrel	OK	345
wasm-release	OK	164

Exports:addCustomReaction annotateKoClass annotateOrigin buildCompoundEgoNetwork buildCrossSpeciesNetwork buildEgoNetwork buildKeggNetwork clusterNetwork combineNetworks convertGene enrichmentDotPlot enrichPathway findKeggIDs findMappedNodes findShortestPaths getPathIDs mapReaction networkDistances networkSimilarity permutePaths removeDrugs removeNetworkNodes replaceNode suggestEntities viewClusterCy viewNetworkCy viewNetworkR

Dependencies:AnnotationDbi askpass backports base64enc base64url BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob bslib cachem caTools checkmate chron cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table data.tree DBI dbplyr digest dplyr evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggforce ggplot2 ggraph ggrepel glue gplots graph graphlayouts gridExtra gsubfn gtable gtools highr Hmisc hms hoardr htmlTable htmltools htmlwidgets httr httr2 igraph IRanges IRdisplay IRkernel isoband jquerylib jsonlite KEGGgraph KEGGREST KernSmooth knitr labeling lambda.r lattice lifecycle magrittr MASS Matrix memoise mime mygene nnet openssl pbdZMQ pillar pkgconfig plyr png polyclip prettyunits progress proto purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl RCy3 repr restfulr Rgraphviz Rhtslib rjson RJSONIO rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer rvest S4Vectors S7 sass scales selectr Seqinfo snow sqldf stringi stringr sys systemfonts tibble tidygraph tidyr tidyselect tinytex tweenr txdbmaker UCSC.utils utf8 uuid vctrs viridis viridisLite webchem withr xfun XML xml2 XVector yaml

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

Rendered fromMetaPathNet-choline-TMA-TMAO.Rmdusingknitr::rmarkdown

Last update: 2026-07-28
Started: 2026-04-30

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

Package: MetaPathNet 0.99.5

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

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Help Manual

Usage by other packages (reverse dependencies)