{
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  "Package": "influential",
  "Type": "Package",
  "Title": "Identification and Classification of the Most Influential Nodes",
  "Language": "en-US",
  "Version": "2.3.3",
  "Authors@R": "c(\nperson(\"Adrian\", \"Salavaty\",\nrole = c(\"aut\", \"cre\"),\nemail = \"abbas.salavaty@gmail.com\",\ncomment = c(ORCID = \"0000-0001-9320-5889\")),\nperson(\"Mirana\", \"Ramialison\", role = \"ths\"),\nperson(c(\"Peter\", \"D.\"), \"Currie\", role = \"ths\")\n)",
  "Description": "Provides functions for the identification, classification,\nand ranking of influential nodes and candidate features from\nnetwork and omics data. The package implements the Integrated\nValue of Influence (IVI) for integrative network centrality\nanalysis, the SIR-based Influence Ranking (SIRIR) model for\nunsupervised influence ranking, and the Experimental data-based\nIntegrative Ranking (ExIR) model for prioritizing candidate\ndriver, biomarker, and mediator features from experimental\nomics data. Functions are provided for network reconstruction\nfrom adjacency matrices and data frames, topological analysis,\ncentrality calculation, assessment of associations between\ncentrality measures, and conditional probability analysis. ExIR\nsupports bulk and single-cell omics data, including matrices,\nsparse matrices, data frames, tibbles, and Seurat objects.",
  "URL": "https://github.com/asalavaty/influential,\nhttps://asalavaty.github.io/influential/",
  "BugReports": "https://github.com/asalavaty/influential/issues",
  "License": "GPL-3",
  "Encoding": "UTF-8",
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  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev",
  "Repository": "https://asalavaty.r-universe.dev",
  "Date/Publication": "2026-10-06 22:57:25 UTC",
  "RemoteUrl": "https://github.com/asalavaty/influential",
  "RemoteRef": "HEAD",
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  "Packaged": {
    "Date": "2026-10-07 09:22:40 UTC",
    "User": "root"
  },
  "Author": "Adrian Salavaty [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9320-5889>),\nMirana Ramialison [ths],\nPeter D. Currie [ths]",
  "Maintainer": "Adrian Salavaty <abbas.salavaty@gmail.com>",
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  "_expires": "2027-01-15T11:29:05.000Z",
  "_created": "2026-10-07T09:22:40.000Z",
  "_published": "2026-10-07T11:29:07.430Z",
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    "collective.influence",
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    "diff_data.assembly",
    "double.cent.assess",
    "double.cent.assess.noRegression",
    "exir",
    "exir.vis",
    "fcor",
    "graph_from_adjacency_matrix",
    "graph_from_data_frame",
    "graph_from_incidence_matrix",
    "h_index",
    "hubness.score",
    "ivi",
    "ivi.from.indices",
    "lh_index",
    "neighborhood.connectivity",
    "runShinyApp",
    "sif2igraph",
    "sirir",
    "spreading.score",
    "V"
  ],
  "_datasets": [
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      "title": "Centrality measures dataset",
      "object": "centrality.measures",
      "class": [
        "data.frame"
      ],
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        "DC",
        "CR",
        "NC",
        "LH_index",
        "BC",
        "CI"
      ],
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      ],
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      "rows": 794,
      "table": true,
      "tojson": true
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      "object": "coexpression.data",
      "class": [
        "data.frame"
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      ],
      "rows": 2410,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "betweenness",
      "title": "Vertex betweenness centrality",
      "concept": [
        "centrality functions"
      ],
      "topics": [
        "BC",
        "betweenness"
      ]
    },
    {
      "page": "cent_network.vis",
      "title": "Centrality-based network visualization",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "cent_network.vis"
      ]
    },
    {
      "page": "centrality.measures",
      "title": "Centrality measures dataset",
      "topics": [
        "centrality.measures"
      ]
    },
    {
      "page": "clusterRank",
      "title": "ClusterRank (CR)",
      "concept": [
        "centrality functions"
      ],
      "topics": [
        "clusterRank",
        "CR"
      ]
    },
    {
      "page": "coexpression.adjacency",
      "title": "Adjacency matrix",
      "topics": [
        "coexpression.adjacency"
      ]
    },
    {
      "page": "coexpression.data",
      "title": "Co-expression dataset",
      "topics": [
        "coexpression.data"
      ]
    },
    {
      "page": "collective.influence",
      "title": "Collective Influence (CI)",
      "concept": [
        "centrality functions"
      ],
      "topics": [
        "CI",
        "collective.influence"
      ]
    },
    {
      "page": "comp_manipulate",
      "title": "Computational manipulation of cells",
      "concept": [
        "integrative ranking functions"
      ],
      "topics": [
        "comp_manipulate"
      ]
    },
    {
      "page": "cond.prob.analysis",
      "title": "Conditional probability of deviation from means",
      "concept": [
        "centrality association assessment functions"
      ],
      "topics": [
        "cond.prob.analysis",
        "CPA"
      ]
    },
    {
      "page": "diff_data.assembly",
      "title": "Assembling the differential/regression data",
      "topics": [
        "DDA",
        "diff_data.assembly"
      ]
    },
    {
      "page": "double.cent.assess",
      "title": "Assessment of innate features and associations of two network centrality measures (dependent and independent)",
      "concept": [
        "centrality association assessment functions"
      ],
      "topics": [
        "DCA",
        "double.cent.assess"
      ]
    },
    {
      "page": "double.cent.assess.noRegression",
      "title": "Assessment of innate features and associations of two network centrality measures",
      "concept": [
        "centrality association assessment functions"
      ],
      "topics": [
        "DCANR",
        "double.cent.assess.noRegression"
      ]
    },
    {
      "page": "exir",
      "title": "Experimental data-based Integrated Ranking",
      "concept": [
        "integrative ranking functions"
      ],
      "topics": [
        "ExIR",
        "exir"
      ]
    },
    {
      "page": "exir.vis",
      "title": "Visualization of ExIR results",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "exir.vis"
      ]
    },
    {
      "page": "fcor",
      "title": "Fast correlation and mutual rank analysis",
      "topics": [
        "fcor"
      ]
    },
    {
      "page": "h_index",
      "title": "H-index",
      "concept": [
        "centrality functions"
      ],
      "topics": [
        "h.index",
        "h_index"
      ]
    },
    {
      "page": "hubness.score",
      "title": "Hubness score",
      "concept": [
        "integrative ranking functions"
      ],
      "topics": [
        "hubness.score"
      ]
    },
    {
      "page": "ivi",
      "title": "Integrated Value of Influence (IVI)",
      "concept": [
        "integrative ranking functions"
      ],
      "topics": [
        "IVI",
        "ivi"
      ]
    },
    {
      "page": "ivi.from.indices",
      "title": "Integrated Value of Influence (IVI)",
      "concept": [
        "integrative ranking functions"
      ],
      "topics": [
        "IVI.FI",
        "ivi.from.indices"
      ]
    },
    {
      "page": "lh_index",
      "title": "local H-index (LH-index)",
      "concept": [
        "centrality functions"
      ],
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        "lh.index",
        "lh_index"
      ]
    },
    {
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      "title": "Neighborhood connectivity",
      "concept": [
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        "NC",
        "neighborhood.connectivity"
      ]
    },
    {
      "page": "runShinyApp",
      "title": "Run shiny app",
      "topics": [
        "runShinyApp"
      ]
    },
    {
      "page": "sif2igraph",
      "title": "SIF to igraph",
      "concept": [
        "network_reconstruction functions"
      ],
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        "sif2igraph"
      ]
    },
    {
      "page": "sirir",
      "title": "SIR-based Influence Ranking",
      "concept": [
        "centrality functions"
      ],
      "topics": [
        "SIRIR",
        "sirir"
      ]
    },
    {
      "page": "spreading.score",
      "title": "Spreading score",
      "concept": [
        "integrative ranking functions"
      ],
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      ]
    }
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      "title": "Introduction to influential",
      "author": "r paste(\"Adrian Salavaty\",strftime(Sys.time(),format=\"%d-%b-%Y\"))",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Package workflows",
        "Featured methods",
        "Fast correlation analysis",
        "Network reconstruction",
        "From a data frame",
        "From an adjacency matrix",
        "From an incidence matrix",
        "From a SIF file",
        "Calculation of centrality measures",
        "Network vertices",
        "Degree centrality",
        "Betweenness centrality",
        "Neighborhood connectivity",
        "H-index",
        "Local H-index",
        "Collective Influence",
        "ClusterRank",
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        "Conditional probability of deviation from means",
        "Nature of association (considering dependent and independent)",
        "Nature of association (without considering dependence direction)",
        "Identification of the most influential network nodes",
        "Integrated Value of Influence (IVI) from centrality measures",
        "Integrated Value of Influence (IVI) from a graph",
        "Network visualization",
        "IVI shiny app",
        "Identification of the most important network spreaders",
        "Identification of the most important network hubs",
        "Ranking the influence of nodes on the topology of a network based on the SIRIR model",
        "Experimental data-based classification and ranking of top candidate features",
        "Preparing the differential/regression data",
        "Assembling the Diff_data",
        "Preparing the experimental data (Exptl_data)",
        "Optional pseudo-sampling for large datasets",
        "Conservative feature filtering",
        "Running the ExIR model",
        "Running exir on single-cell RNA-seq data",
        "ExIR visualization",
        "ExIR shiny app",
        "Computational manipulation of cells",
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      "created": "2020-01-16 03:58:25",
      "modified": "2026-08-21 00:54:54",
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