{
  "_id": "6a1bcf621d7bb097a0a1403c",
  "Package": "NetPathMiner",
  "Version": "1.49.1",
  "Date": "2014 onwards",
  "Title": "NetPathMiner for Biological Network Construction, Path Mining\nand Visualization",
  "Authors@R": "c(\nperson(\"Ahmed\", \"Mohamed\", , \"mohamed@kuicr.kyoto-u.ac.jp\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-6507-5300\")),\nperson(\"Tim\", \"Hancock\", , \"timothy.hancock@kuicr.kyoto-u.ac.jp\", role = c(\"aut\")),\nperson(\"Tim\", \"Hancock\", , \"timothy.hancock@kuicr.kyoto-u.ac.jp\", role = c(\"aut\"))\n)",
  "Description": "NetPathMiner is a general framework for network path\nmining using genome-scale networks. It constructs networks from\nKGML, SBML and BioPAX files, providing three network\nrepresentations, metabolic, reaction and gene representations.\nNetPathMiner finds active paths and applies machine learning\nmethods to summarize found paths for easy interpretation. It\nalso provides static and interactive visualizations of networks\nand paths to aid manual investigation.",
  "VignetteBuilder": "knitr",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/ahmohamed/NetPathMiner",
  "NeedsCompilation": "yes",
  "SystemRequirements": "libxml2, libSBML (>= 5.5)",
  "Biarch": "TRUE",
  "biocViews": "GraphAndNetwork, Pathways, Network, Clustering,\nClassification",
  "RoxygenNote": "7.2.3",
  "Encoding": "UTF-8",
  "Config/Bioconductor/UnsupportedPlatforms": "windows",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-29 18:37:07 UTC",
  "RemoteUrl": "https://github.com/bioc/NetPathMiner",
  "RemoteRef": "HEAD",
  "RemoteSha": "0421150dede87b90971ec447d8dccb263e0401e9",
  "Packaged": {
    "Date": "2026-05-29 21:57:15 UTC",
    "User": "root"
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  "Author": "Ahmed Mohamed [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6507-5300>),\nTim Hancock [aut],\nTim Hancock [aut]",
  "Maintainer": "Ahmed Mohamed <mohamed@kuicr.kyoto-u.ac.jp>",
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  "_created": "2026-05-29T21:57:15.000Z",
  "_published": "2026-05-31T06:04:18.512Z",
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    "author": "A Wokaty <awokaty@users.noreply.github.com>",
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    "email": "mohamed@kuicr.kyoto-u.ac.jp",
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    "description": "Ph.D. in Bioinformatics and chemical genomics (Kyoto Uni) interested in developing highly extensible easy-to-use scientific applications.",
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    "network",
    "clustering",
    "classification",
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    "extra/citation.json",
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  "_exports": [
    "assignEdgeWeights",
    "biopax2igraph",
    "colorVertexByAttr",
    "expandComplexes",
    "extractPathNetwork",
    "fetchAttribute",
    "getAttribute",
    "getAttrNames",
    "getAttrStatus",
    "getGeneSetNetworks",
    "getGeneSets",
    "getPathsAsEIDs",
    "KGML2igraph",
    "layoutVertexByAttr",
    "makeGeneNetwork",
    "makeMetaboliteNetwork",
    "makeReactionNetwork",
    "NPMdefaults",
    "pathClassifier",
    "pathCluster",
    "pathRanker",
    "pathsToBinary",
    "plotAllNetworks",
    "plotClassifierROC",
    "plotClusterMatrix",
    "plotClusterProbs",
    "plotClusters",
    "plotCytoscapeGML",
    "plotNetwork",
    "plotPathClassifier",
    "plotPathCluster",
    "plotPaths",
    "predictPathClassifier",
    "predictPathCluster",
    "registerMemoryErr",
    "reindexNetwork",
    "rmAttribute",
    "rmSmallCompounds",
    "SBML2igraph",
    "setAttribute",
    "simplifyReactionNetwork",
    "stdAttrNames",
    "toGraphNEL",
    "vertexDeleteReconnect"
  ],
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      "title": "Biopax example data",
      "object": "ex_biopax",
      "file": "ex_biopax.rda",
      "class": [
        "biopax",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ex_kgml_sig",
      "title": "Singaling network from KGML example",
      "object": "ex_kgml_sig",
      "file": "ex_kgml_sig.rda",
      "class": [
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ex_microarray",
      "title": "An microarray data example.",
      "object": "ex_microarray",
      "file": "ex_microarray.rda",
      "class": [
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      ],
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      "table": true,
      "tojson": true
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    {
      "name": "ex_sbml",
      "title": "Metabolic network from SBML example",
      "object": "ex_sbml",
      "file": "ex_sbml.rda",
      "class": [
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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  ],
  "_help": [
    {
      "page": "NetPathMiner-package",
      "title": "General framework for network extraction, path mining.",
      "topics": [
        "NetPathMiner-package",
        "NetPathMiner",
        "NPM"
      ]
    },
    {
      "page": "assignEdgeWeights",
      "title": "Assigning weights to network edges",
      "topics": [
        "assignEdgeWeights"
      ]
    },
    {
      "page": "biopax2igraph",
      "title": "Processes BioPAX objects into igraph objects",
      "concept": [
        "Database extraction methods"
      ],
      "topics": [
        "biopax2igraph"
      ]
    },
    {
      "page": "colorVertexByAttr",
      "title": "Computes colors for vertices according to their attributes.",
      "concept": [
        "Plotting methods"
      ],
      "topics": [
        "colorVertexByAttr"
      ]
    },
    {
      "page": "ex_biopax",
      "title": "Biopax example data",
      "topics": [
        "ex_biopax"
      ]
    },
    {
      "page": "ex_kgml_sig",
      "title": "Singaling network from KGML example",
      "topics": [
        "ex_kgml_sig"
      ]
    },
    {
      "page": "ex_microarray",
      "title": "An microarray data example.",
      "topics": [
        "ex_microarray"
      ]
    },
    {
      "page": "ex_sbml",
      "title": "Metabolic network from SBML example",
      "topics": [
        "ex_sbml"
      ]
    },
    {
      "page": "makeGeneNetwork",
      "title": "Expand reactions / complexes into their gene constituents.",
      "concept": [
        "Network processing methods"
      ],
      "topics": [
        "expandComplexes",
        "makeGeneNetwork"
      ]
    },
    {
      "page": "extractPathNetwork",
      "title": "Creates a subnetwork from a ranked path list",
      "concept": [
        "Path ranking methods"
      ],
      "topics": [
        "extractPathNetwork"
      ]
    },
    {
      "page": "getAttr",
      "title": "Get / Set vertex attribute names and coverage",
      "concept": [
        "Attribute handling methods"
      ],
      "topics": [
        "getAttribute",
        "getAttrNames",
        "getAttrStatus",
        "rmAttribute",
        "setAttribute"
      ]
    },
    {
      "page": "getGeneSetNetworks",
      "title": "Generate geneset networks from an annotated network.",
      "topics": [
        "getGeneSetNetworks"
      ]
    },
    {
      "page": "getGeneSets",
      "title": "Generate genesets from an annotated network.",
      "topics": [
        "getGeneSets"
      ]
    },
    {
      "page": "getPathsAsEIDs",
      "title": "Convert a ranked path list to edge ids of a graph",
      "concept": [
        "Path ranking methods"
      ],
      "topics": [
        "getPathsAsEIDs"
      ]
    },
    {
      "page": "KGML2igraph",
      "title": "Processes KGML files into igraph objects",
      "concept": [
        "Database extraction methods"
      ],
      "topics": [
        "KGML2igraph"
      ]
    },
    {
      "page": "layoutVertexByAttr",
      "title": "A graph layout function, which groups vertices by attribute.",
      "concept": [
        "Plotting methods"
      ],
      "topics": [
        "layoutVertexByAttr"
      ]
    },
    {
      "page": "makeMetaboliteNetwork",
      "title": "Convert metabolic network to metabolite network.",
      "concept": [
        "Network processing methods"
      ],
      "topics": [
        "makeMetaboliteNetwork"
      ]
    },
    {
      "page": "makeReactionNetwork",
      "title": "Convert metabolic network to reaction network.",
      "concept": [
        "Network processing methods"
      ],
      "topics": [
        "makeReactionNetwork"
      ]
    },
    {
      "page": "NPMdefaults",
      "title": "Default values for NetPathMiner",
      "topics": [
        "NPMdefaults"
      ]
    },
    {
      "page": "pathClassifier",
      "title": "HME3M Markov pathway classifier.",
      "concept": [
        "Path clustering & classification methods"
      ],
      "topics": [
        "pathClassifier"
      ]
    },
    {
      "page": "pathCluster",
      "title": "3M Markov mixture model for clustering pathways",
      "concept": [
        "Path clustering & classification methods"
      ],
      "topics": [
        "pathCluster"
      ]
    },
    {
      "page": "pathRanker",
      "title": "Extracting and ranking paths from a network",
      "concept": [
        "Path ranking methods"
      ],
      "topics": [
        "pathRanker"
      ]
    },
    {
      "page": "pathsToBinary",
      "title": "Converts the result from pathRanker into something suitable for pathClassifier or pathCluster.",
      "concept": [
        "Path clustering & classification methods"
      ],
      "topics": [
        "pathsToBinary"
      ]
    },
    {
      "page": "plotAllNetworks",
      "title": "Higlighting ranked paths over multiple network representations.",
      "concept": [
        "Plotting methods"
      ],
      "topics": [
        "plotAllNetworks"
      ]
    },
    {
      "page": "plotClassifierROC",
      "title": "Diagnostic plots for pathClassifier.",
      "concept": [
        "Path clustering & classification methods",
        "Plotting methods"
      ],
      "topics": [
        "plotClassifierROC"
      ]
    },
    {
      "page": "plotClusters",
      "title": "Plots the structure of all path clusters",
      "concept": [
        "Path clustering & classification methods",
        "Plotting methods"
      ],
      "topics": [
        "plotClusterMatrix",
        "plotClusterProbs",
        "plotClusters"
      ]
    },
    {
      "page": "plotCytoscape",
      "title": "Plots an annotated igraph object in Cytoscape.",
      "concept": [
        "Plotting methods"
      ],
      "topics": [
        "plotCytoscapeGML"
      ]
    },
    {
      "page": "plotNetwork",
      "title": "Plots an annotated igraph object.",
      "concept": [
        "Plotting methods"
      ],
      "topics": [
        "plotNetwork"
      ]
    },
    {
      "page": "plotPathClassifier",
      "title": "Plots the structure of specified path found by pathClassifier.",
      "concept": [
        "Path clustering & classification methods",
        "Plotting methods"
      ],
      "topics": [
        "plotPathClassifier"
      ]
    },
    {
      "page": "plotPathCluster",
      "title": "Plots the structure of specified path cluster",
      "concept": [
        "Path clustering & classification methods"
      ],
      "topics": [
        "plotPathCluster"
      ]
    },
    {
      "page": "plotPaths",
      "title": "Plots an annotated igraph object higlighting ranked paths.",
      "concept": [
        "Plotting methods"
      ],
      "topics": [
        "plotPaths"
      ]
    },
    {
      "page": "predictPathClassifier",
      "title": "Predicts new paths given a pathClassifier model.",
      "concept": [
        "Path clustering & classification methods"
      ],
      "topics": [
        "predictPathClassifier"
      ]
    },
    {
      "page": "predictPathCluster",
      "title": "Predicts new paths given a pathCluster model",
      "concept": [
        "Path clustering & classification methods"
      ],
      "topics": [
        "predictPathCluster"
      ]
    },
    {
      "page": "registerMemoryErr",
      "title": "Internal method to register memery errors.",
      "topics": [
        "registerMemoryErr"
      ]
    },
    {
      "page": "reindexNetwork",
      "title": "Replaces current vertex ids with chosen attribute.",
      "concept": [
        "Network processing methods"
      ],
      "topics": [
        "reindexNetwork"
      ]
    },
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      "page": "rmSmallCompounds",
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      "filename": "NPMVignette.html",
      "title": "Workflow for NetPathMiner",
      "author": "Ahmed Mohamed",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Version Info",
        "Introduction",
        "Installation Instructions",
        "System Prerequisites",
        "Prerequisites for Unix users (Linux and Mac OS)",
        "Installing libxml2",
        "Installing libSBML",
        "Prerequisites for Windows users",
        "R Package dependencies",
        "igraph",
        "devtools",
        "RCurl",
        "rBiopaxParser",
        "NetPathMiner Installation",
        "From Bioconductor:",
        "From GitHub using devtools:",
        "Getting Started",
        "Database Extraction",
        "Handling Annotation Attributes",
        "Network Processing",
        "Weighting Network",
        "Path Ranking",
        "Clustering and classification of paths",
        "Plotting",
        "Additional functions",
        "Genesets and geneset subnetworks",
        "Integration with graph package"
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      "created": "2019-03-02 12:45:08",
      "modified": "2019-04-01 06:41:42",
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