{
  "_id": "6a4b54a6a6574ff277f99a88",
  "Package": "NTW",
  "Type": "Package",
  "Title": "Predict gene network using an Ordinary Differential Equation\n(ODE) based method",
  "Version": "1.63.0",
  "Date": "2011-10-8",
  "Author": "Wei Xiao, Yin Jin, Darong Lai, Xinyi Yang, Yuanhua Liu,\nChristine Nardini",
  "Maintainer": "Yuanhua Liu <liuyuanhua@picb.ac.cn>",
  "Description": "This package predicts the gene-gene interaction network\nand identifies the direct transcriptional targets of the\nperturbation using an ODE (Ordinary Differential Equation)\nbased method.",
  "License": "GPL-2",
  "biocViews": "Preprocessing",
  "LazyLoad": "yes",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:43 UTC",
  "RemoteUrl": "https://github.com/bioc/NTW",
  "RemoteRef": "HEAD",
  "RemoteSha": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-06 07:06:25 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "NTW_1.63.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/c09a9c6610edf651e7a2e9ec99f953d7b415ade57cc72ae526e39c2ca8883d83",
  "_filesize": 882323,
  "_sha256": "c09a9c6610edf651e7a2e9ec99f953d7b415ade57cc72ae526e39c2ca8883d83",
  "_expires": "2026-10-14T07:09:24.000Z",
  "_created": "2026-07-06T07:06:25.000Z",
  "_published": "2026-07-06T07:09:26.433Z",
  "_bioccheck": {
    "error": 2,
    "warning": 2,
    "note": 11
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28773905973",
  "_status": "success",
  "_upstream": "https://github.com/bioc/NTW",
  "_commit": {
    "id": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379683
  },
  "_maintainer": {
    "name": "Yuanhua Liu",
    "email": "liuyuanhua@picb.ac.cn"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85313893423,
      "time": 133,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8101941090"
    },
    {
      "job": 85313893447,
      "time": 145,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8101944223"
    },
    {
      "job": 85313893435,
      "time": 128,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8101939818"
    },
    {
      "job": 85313893411,
      "time": 85,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8101926468"
    },
    {
      "job": 85313893437,
      "time": 67,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8101921566"
    },
    {
      "job": 85313474117,
      "time": 168,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8101900774"
    },
    {
      "job": 85313893431,
      "time": 117,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8101935950"
    },
    {
      "job": 85313893440,
      "time": 77,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8101924452"
    },
    {
      "job": 85313893452,
      "time": 62,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8101919980"
    },
    {
      "job": 85313893441,
      "time": 62,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8101920055"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.3.0",
      "role": "Depends"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.63.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.62.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "preprocessing"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 3,
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/NTW.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "A.estimation.Srow",
    "AP.estimation.Srow",
    "backward",
    "comb.matrix",
    "forward",
    "method.geo",
    "method.ml",
    "method.sse",
    "NTW",
    "P.preestimation"
  ],
  "_datasets": [
    {
      "name": "sos.data",
      "title": "SOS pathway perturbation data",
      "object": "sos.data",
      "file": "sos.data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "p.recA",
        "p.lexA",
        "p.ssb",
        "p.recF",
        "p.dinI",
        "p.umuDC",
        "p.rpoD",
        "p.rpoH",
        "p.rpoS"
      ],
      "rows": 9,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "NTW-package",
      "title": "Gene interaction network and perturbation targets predictions",
      "topics": [
        "NTW-package"
      ]
    },
    {
      "page": "A.estimation.Srow",
      "title": "Estimation of a single row in matrix A with the perturbation targets matrix P known",
      "topics": [
        "A.estimation.Srow"
      ]
    },
    {
      "page": "AP.estimation.Srow",
      "title": "Estimation of a single row in gene interaction matrix A and perturbation targets matrix P",
      "topics": [
        "AP.estimation.Srow"
      ]
    },
    {
      "page": "comb.matrix",
      "title": "Create all combinations of vectors",
      "topics": [
        "comb.matrix"
      ]
    },
    {
      "page": "methods.regression",
      "title": "Regression methods to estimate a single row in A with fixed perturbations",
      "topics": [
        "method.geo",
        "method.ml",
        "method.sse"
      ]
    },
    {
      "page": "NTW",
      "title": "Estimation of gene interaction matrix A and perturbation targets matrix P",
      "topics": [
        "NTW"
      ]
    },
    {
      "page": "P.preestimation",
      "title": "Pre-estimation of the transcriptional pertubation targets matrix P",
      "topics": [
        "P.preestimation"
      ]
    },
    {
      "page": "patterns.priorA",
      "title": "Approaches to use a priori known gene association information for a single row estimation in matrix A",
      "topics": [
        "backward",
        "forward"
      ]
    },
    {
      "page": "sos.data",
      "title": "SOS pathway perturbation data",
      "topics": [
        "sos.data"
      ]
    }
  ],
  "_rundeps": [
    "mvtnorm"
  ],
  "_vignettes": [
    {
      "source": "NTW.Rnw",
      "filename": "NTW.pdf",
      "title": "NTW vignette",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Beginning NTW"
      ],
      "created": "2013-11-01 20:13:51",
      "modified": "2013-11-01 20:13:51",
      "commits": 1
    }
  ],
  "_score": 3.778151250383644,
  "_indexed": true,
  "_nocasepkg": "ntw",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.63.0",
      "date": "2026-07-06T07:08:52.000Z",
      "distro": "resolute",
      "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3",
      "fileid": "https://r2.ropensci.org/795ba0d33fc440b80ddd8b0bd92f7b98a02fa06661a2528a933766000dddd47a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28773905973"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.63.0",
      "date": "2026-07-06T07:08:36.000Z",
      "distro": "resolute",
      "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3",
      "fileid": "https://r2.ropensci.org/1f25994f3ccd527a60d2fa8afe227f0b370c865ca09db25340461c727a39cfc5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28773905973"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.63.0",
      "date": "2026-07-06T07:07:54.000Z",
      "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3",
      "fileid": "https://r2.ropensci.org/b28f5401da14b4d9ed5412b951afb9729c1b104ae8307d42ce230237abece6fd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28773905973"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.63.0",
      "date": "2026-07-06T07:07:40.000Z",
      "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3",
      "fileid": "https://r2.ropensci.org/7c487d7cd36289afe97c4bd077606f35a4e49d1b824bc428976f68f0a0bf3f97",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28773905973"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.63.0",
      "date": "2026-07-06T07:08:38.000Z",
      "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3",
      "fileid": "https://r2.ropensci.org/1700d18024ea8421f53220f0a867aee506800626ace0184ad5dd1ebc1d4e5a1f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28773905973"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.63.0",
      "date": "2026-07-06T07:07:39.000Z",
      "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3",
      "fileid": "https://r2.ropensci.org/045615f1d10e738ab02cd8a059a4978568f72293ee501729d7743b5a4e00d298",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28773905973"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.63.0",
      "date": "2026-07-06T07:07:24.000Z",
      "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3",
      "fileid": "https://r2.ropensci.org/de87ed4e56731a77d52f2e4d0f3d62c9242a878498ddd24c2ce1d375303cc253",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28773905973"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.63.0",
      "date": "2026-07-06T07:07:25.000Z",
      "commit": "5e5ce3152b5c5453fff99dd89982c5a96d3496e3",
      "fileid": "https://r2.ropensci.org/17222dd13ca74fc4d44423e99be3aa4f58f564451b469c80a7a13ca51d13d04f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28773905973"
    }
  ]
}