{
  "_id": "6a1ffe3db401979e7344534a",
  "Package": "ExpressionCellNet",
  "Type": "Package",
  "Title": "Network-Based Analysis of Gene Expression Perturbations",
  "Version": "0.1.1",
  "Authors@R": "person(\"Ehsan\", \"Keramati\", email = \"ehsan.keramati14@gmail.com\", role = c(\"aut\", \"cre\"))",
  "Description": "Network-centric framework for integrative analysis of\nhigh-throughput gene expression data using user-supplied\ngene-gene interaction graphs. Constructs seed-centered\nmulti-generation networks constrained by expression\ncorrelations and simulates expression perturbation scenarios\nvia regression-based prediction (van Dam, 2018).",
  "URL": "https://doi.org/10.1093/bib/bbw139",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 10:09:56 UTC",
    "User": "root"
  },
  "Author": "Ehsan Keramati [aut, cre]",
  "Maintainer": "Ehsan Keramati <ehsan.keramati14@gmail.com>",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://ehsankeramatii.r-universe.dev",
  "Date/Publication": "2026-03-04 09:50:13 UTC",
  "RemoteUrl": "https://github.com/cran/ExpressionCellNet",
  "RemoteRef": "HEAD",
  "RemoteSha": "54e4ddcb706ef89cc68f7ec3deab2b373958c61c",
  "MD5sum": "5adc0ad8494d513471ee7da4ba087b5f",
  "_user": "ehsankeramatii",
  "_type": "src",
  "_file": "ExpressionCellNet_0.1.1.tar.gz",
  "_fileid": "1febaa8724eb939c02e0f8a7fc9d5f4e1154c09b842935c23d974e90ca89207c",
  "_filesize": 149323,
  "_sha256": "1febaa8724eb939c02e0f8a7fc9d5f4e1154c09b842935c23d974e90ca89207c",
  "_created": "2026-06-03T10:09:56.000Z",
  "_published": "2026-06-03T10:13:17.050Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79270595973,
      "time": 138,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7381728040"
    },
    {
      "job": 79270595882,
      "time": 136,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7381727226"
    },
    {
      "job": 79270596254,
      "time": 161,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7381728258"
    },
    {
      "job": 79270596498,
      "time": 165,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7381725801"
    },
    {
      "job": 79270036456,
      "time": 193,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7381676595"
    },
    {
      "job": 79270595956,
      "time": 120,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7381721756"
    },
    {
      "job": 79270596164,
      "time": 102,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7381715402"
    },
    {
      "job": 79270596094,
      "time": 102,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7381715091"
    },
    {
      "job": 79270596211,
      "time": 103,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7381715683"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ehsankeramatii/actions/runs/26877891279",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/ExpressionCellNet",
  "_commit": {
    "id": "54e4ddcb706ef89cc68f7ec3deab2b373958c61c",
    "author": "Ehsan Keramati <ehsan.keramati14@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.1\n",
    "time": 1772617813
  },
  "_maintainer": {
    "name": "Ehsan Keramati",
    "email": "ehsan.keramati14@gmail.com",
    "login": "ehsankeramatii",
    "description": "",
    "uuid": 66267856
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "uwot",
      "role": "Imports"
    },
    {
      "package": "Metrics",
      "role": "Imports"
    },
    {
      "package": "crayon",
      "role": "Imports"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-10",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.1.1",
      "date": "2026-03-04"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "ehsankeramatii",
      "count": 1,
      "uuid": 66267856
    }
  ],
  "_userbio": {
    "uuid": 66267856,
    "type": "user",
    "name": "Ehsan Keramati"
  },
  "_downloads": {
    "count": 442,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ExpressionCellNet"
  },
  "_searchresults": 0,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/ExpressionCellNet.html",
    "manual.pdf"
  ],
  "_realowner": "ehsankeramatii",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.1",
      "date": "2026-03-04"
    }
  ],
  "_exports": [
    "AnalyzeNetwork",
    "BuildNetwork",
    "CountMatrixNormalization",
    "createExpCellNetObj",
    "ExtractFeature",
    "FindPathway",
    "MeanExpression",
    "NetworkPrediction",
    "PCAforGenes",
    "PlotCorrelation",
    "PlotCountMatrix",
    "PlotNetworkPrediction",
    "PlotPathwayPrediction",
    "RegenerateTrainTest",
    "ShowHubGenes",
    "ShowNetwork",
    "ShowPathway",
    "UMAPforGenes"
  ],
  "_datasets": [
    {
      "name": "example_data",
      "title": "Example dataset for ExpressionCellNet",
      "object": "example_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "AnalyzeNetwork",
      "title": "Analyze network topology and identify hub genes",
      "topics": [
        "AnalyzeNetwork"
      ]
    },
    {
      "page": "BuildNetwork",
      "title": "Construct a gene interaction network centered on a seed gene",
      "topics": [
        "BuildNetwork"
      ]
    },
    {
      "page": "CountMatrixNormalization",
      "title": "Normalize expression count matrix",
      "topics": [
        "CountMatrixNormalization"
      ]
    },
    {
      "page": "createExpCellNetObj",
      "title": "Create an ExpressionCellNet object",
      "topics": [
        "createExpCellNetObj"
      ]
    },
    {
      "page": "example_data",
      "title": "Example dataset for ExpressionCellNet",
      "topics": [
        "example_data"
      ]
    },
    {
      "page": "ExtractFeature",
      "title": "Extract network-derived expression features",
      "topics": [
        "ExtractFeature"
      ]
    },
    {
      "page": "FindPathway",
      "title": "Find the shortest path between two genes in the network",
      "topics": [
        "FindPathway"
      ]
    },
    {
      "page": "MeanExpression",
      "title": "Compute mean expression of a gene",
      "topics": [
        "MeanExpression"
      ]
    },
    {
      "page": "NetworkPrediction",
      "title": "Predict network-wide expression changes after perturbing a seed gene",
      "topics": [
        "NetworkPrediction"
      ]
    },
    {
      "page": "PCAforGenes",
      "title": "PCA on network-derived features",
      "topics": [
        "PCAforGenes"
      ]
    },
    {
      "page": "PlotCorrelation",
      "title": "Plot correlation between two genes",
      "topics": [
        "PlotCorrelation"
      ]
    },
    {
      "page": "PlotCountMatrix",
      "title": "Plot expression matrix distribution",
      "topics": [
        "PlotCountMatrix"
      ]
    },
    {
      "page": "PlotNetworkPrediction",
      "title": "Plot network prediction summary",
      "topics": [
        "PlotNetworkPrediction"
      ]
    },
    {
      "page": "PlotPathwayPrediction",
      "title": "Plot pathway-restricted prediction to a target gene",
      "topics": [
        "PlotPathwayPrediction"
      ]
    },
    {
      "page": "RegenerateTrainTest",
      "title": "Regenerate train/test split",
      "topics": [
        "RegenerateTrainTest"
      ]
    },
    {
      "page": "ShowHubGenes",
      "title": "Show hub genes on the network",
      "topics": [
        "ShowHubGenes"
      ]
    },
    {
      "page": "ShowNetwork",
      "title": "Visualize the constructed network",
      "topics": [
        "ShowNetwork"
      ]
    },
    {
      "page": "ShowPathway",
      "title": "Visualize a pathway (highlighted subgraph)",
      "topics": [
        "ShowPathway"
      ]
    },
    {
      "page": "UMAPforGenes",
      "title": "UMAP on network-derived features",
      "topics": [
        "UMAPforGenes"
      ]
    }
  ],
  "_rundeps": [
    "BH",
    "cli",
    "cpp11",
    "crayon",
    "dqrng",
    "farver",
    "FNN",
    "ggplot2",
    "glue",
    "gtable",
    "igraph",
    "irlba",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "Metrics",
    "pkgconfig",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppEigen",
    "RcppProgress",
    "rlang",
    "RSpectra",
    "S7",
    "scales",
    "sitmo",
    "uwot",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 1,
  "_indexed": true,
  "_nocasepkg": "expressioncellnet",
  "_universes": [
    "ehsankeramatii"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-06-03T10:12:17.000Z",
      "distro": "noble",
      "commit": "54e4ddcb706ef89cc68f7ec3deab2b373958c61c",
      "fileid": "0fe54d2bc25493bc14bb7badf907aa5630d195b5cdfe3737057df6de8cfc810b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ehsankeramatii/actions/runs/26877891279"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-06-03T10:12:16.000Z",
      "distro": "noble",
      "commit": "54e4ddcb706ef89cc68f7ec3deab2b373958c61c",
      "fileid": "a33179c8dd79672964a9955cdddd81ebf8ba003eafb1f3a79bc60ae43f1898ee",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ehsankeramatii/actions/runs/26877891279"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-06-03T10:12:24.000Z",
      "commit": "54e4ddcb706ef89cc68f7ec3deab2b373958c61c",
      "fileid": "9226b2b2fb986fb1a3f296530802fdfd69df1e7b6f5c6c70e5580dfdb48ba9e7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ehsankeramatii/actions/runs/26877891279"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-06-03T10:12:16.000Z",
      "commit": "54e4ddcb706ef89cc68f7ec3deab2b373958c61c",
      "fileid": "99683b40d2393e65ef5e3b2ca0f1b650d2406501df4767657bd13032e9f09d64",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ehsankeramatii/actions/runs/26877891279"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.1",
      "date": "2026-06-03T10:12:16.000Z",
      "commit": "54e4ddcb706ef89cc68f7ec3deab2b373958c61c",
      "fileid": "c7a2aa4562cc1ac78e8d854a17520b752954234ea026cd57d2503d543918168a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ehsankeramatii/actions/runs/26877891279"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-06-03T10:11:35.000Z",
      "commit": "54e4ddcb706ef89cc68f7ec3deab2b373958c61c",
      "fileid": "45179b62ce9c8299b7aae13bdac1dc7e0cc4f8b95fdcb90a249c5cbb026af8ce",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ehsankeramatii/actions/runs/26877891279"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-06-03T10:11:30.000Z",
      "commit": "54e4ddcb706ef89cc68f7ec3deab2b373958c61c",
      "fileid": "daaad26524c9aeb5f51d8ce002d6ee6493325e2eb113715872db5ea84647213e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ehsankeramatii/actions/runs/26877891279"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-06-03T10:11:39.000Z",
      "commit": "54e4ddcb706ef89cc68f7ec3deab2b373958c61c",
      "fileid": "fd55fe76a36f637520025dae31e2313c5a6aabcc7746aff3be3497085ef2edc7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ehsankeramatii/actions/runs/26877891279"
    }
  ]
}