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:

On BioConductor:MetaPathNet-0.99.5(bioc 3.24)

networkpathwayskeggsystemsbiologyclassificationmicrobiome

2.90 score 2 stars 597 downloads 27 exports 159 dependencies

Last updated from:fdaae4de76. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

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bioc-checksNOTE217
linux-develWARNING351
source / vignettesERROR442
linux-releaseWARNING463
macos-releaseWARNING443
macos-oldrelWARNING349
windows-develWARNING316
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wasm-releaseOK189

Exports:addCustomReactionannotateKoClassannotateOriginbuildCompoundEgoNetworkbuildCrossSpeciesNetworkbuildEgoNetworkbuildKeggNetworkclusterNetworkcombineNetworksconvertGeneenrichmentDotPlotenrichPathwayfindKeggIDsfindMappedNodesfindShortestPathsgetPathIDsmapReactionnetworkDistancesnetworkSimilaritypermutePathsremoveDrugsremoveNetworkNodesreplaceNodesuggestEntitiesviewClusterCyviewNetworkCyviewNetworkR

Dependencies:AnnotationDbiaskpassbackportsbase64encbase64urlBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcaToolscheckmatechroncigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tabledata.treeDBIdbplyrdigestdplyrevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggplot2ggraphggrepelgluegplotsgraphgraphlayoutsgridExtragsubfngtablegtoolshighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphIRangesIRdisplayIRkernelisobandjquerylibjsonliteKEGGgraphKEGGRESTKernSmoothknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixmemoisemimemygenennetopensslpbdZMQpillarpkgconfigplyrpngpolyclipprettyunitsprogressprotopurrrR6rappdirsRColorBrewerRcppRcppArmadilloRCurlRCy3reprrestfulrRgraphvizRhtslibrjsonRJSONIOrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerrvestS4VectorsS7sassscalesselectrSeqinfosnowsqldfstringistringrsyssystemfontstibbletidygraphtidyrtidyselecttinytextweenrtxdbmakerUCSC.utilsutf8uuidvctrsviridisviridisLitewebchemwithrxfunXMLxml2XVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Build MetaPathNet-style edges from user-defined reactionsaddCustomReaction
Annotate KO functional class (metabolic vs signalling)annotateKoClass
Annotate KO Origin (Host vs Bacteria) and Optionally Export to CytoscapeannotateOrigin
Build compound-centred ego subnetworks across KEGG organismsbuildCompoundEgoNetwork
Build Cross-Species MetaPathNet NetworkbuildCrossSpeciesNetwork
Extract an Ego Subnetwork from a Metabolic / Signalling NetworkbuildEgoNetwork
Build KEGG Metabolic and Signaling NetworkbuildKeggNetwork
Community Detection in KEGG-Derived NetworksclusterNetwork
Merge Multiple MetaPathNet-Style NetworkscombineNetworks
Convert Ensembl or Entrez Gene IDs to KEGG Gene IDs and KO TermsconvertGene
Create a Dot Plot of Pathway Enrichment ResultsenrichmentDotPlot
Pathway Enrichment Analysis on KEGG-Based Node SetsenrichPathway
Find KEGG Identifiers for Compounds, Organisms, and KO TermsfindKeggIDs
Map User-Supplied Nodes to a NetworkfindMappedNodes
Identify Shortest Paths Between Node Sets in a KEGG-Derived NetworkfindShortestPaths
Retrieve and Classify Organism-Specific KEGG PathwaysgetPathIDs
Map reaction IDs to MetaPathNet-style networksmapReaction
Example tryptophan-related MetaPathNet networkMetaPathNet_example_network
Calculate Shortest-Path Distances Between Node Sets in a KEGG-Based NetworknetworkDistances
Compare KEGG-Based Networks via Jaccard SimilaritynetworkSimilarity
Permutation Test of Shortest-Path Structure Between Node SetspermutePaths
Remove Drug Nodes from a Network MatrixremoveDrugs
Remove Specified Nodes from a Network MatrixremoveNetworkNodes
Replace Nodes in a Network TablereplaceNode
Suggest Candidate Prokaryotic Organisms or KOs from KEGG IdentifierssuggestEntities
Visualise Clustered MetaPathNet Networks in CytoscapeviewClusterCy
Visualize a KEGG-Derived Network in Cytoscape via RCy3viewNetworkCy
Visualise a KEGG-Based Network Matrix in RviewNetworkR