{
  "_id": "6a1030f1acfb0bcc41c96448",
  "Package": "DysPIA",
  "Type": "Package",
  "Title": "Dysregulated Pathway Identification Analysis",
  "Version": "1.4",
  "Date": "2020-07-26",
  "Authors@R": "c(person(\"Limei\", \"Wang\", role = c(\"aut\", \"cre\"),\nemail = \"lemon619@gmail.com\"),\nperson(\"Jin\", \"Li\", role = c(\"aut\", \"ctb\"),\nemail = \"lijin0202@gmail.com\"))",
  "Maintainer": "Limei Wang <lemon619@gmail.com>",
  "Description": "It is used to identify dysregulated pathways based on a\npre-ranked gene pair list. A fast algorithm is used to make the\ncomputation really fast. The data in package 'DysPIAData' is\nneeded.",
  "License": "GPL (>= 2)",
  "RoxygenNote": "7.1.1",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Repository": "https://lemonwang2020.r-universe.dev",
  "Date/Publication": "2020-08-03 15:25:44 UTC",
  "RemoteUrl": "https://github.com/lemonwang2020/dyspia",
  "RemoteRef": "HEAD",
  "RemoteSha": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-12 09:16:05 UTC",
    "User": "root"
  },
  "Author": "Limei Wang [aut, cre],\nJin Li [aut, ctb]",
  "MD5sum": "2b67188c15b8accb0f86e033b5396ae8",
  "_user": "lemonwang2020",
  "_type": "src",
  "_file": "DysPIA_1.4.tar.gz",
  "_fileid": "14cba891f2aa87e901e9ec2e0617bf1bf2dbfab73f2c30e4ae421b0c99d34de7",
  "_filesize": 2893480,
  "_sha256": "14cba891f2aa87e901e9ec2e0617bf1bf2dbfab73f2c30e4ae421b0c99d34de7",
  "_created": "2026-05-12T09:16:05.000Z",
  "_published": "2026-05-22T10:33:21.643Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77362453058,
      "time": 120,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6940265201"
    },
    {
      "job": 77362452774,
      "time": 177,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6940285611"
    },
    {
      "job": 77362453303,
      "time": 154,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940275292"
    },
    {
      "job": 77362453085,
      "time": 171,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940283220"
    },
    {
      "job": 77362453107,
      "time": 237,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6940292719"
    },
    {
      "job": 77362453198,
      "time": 166,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6940367504"
    },
    {
      "job": 77362453045,
      "time": 167,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940322291"
    },
    {
      "job": 77362452807,
      "time": 357,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940411147"
    },
    {
      "job": 77362452633,
      "time": 183,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940221398"
    },
    {
      "job": 77362452373,
      "time": 108,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7158431082"
    },
    {
      "job": 77362452828,
      "time": 110,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6940261035"
    },
    {
      "job": 77362453305,
      "time": 144,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6940272079"
    },
    {
      "job": 77362452950,
      "time": 146,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6940272521"
    }
  ],
  "_buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/lemonwang2020/dyspia",
  "_commit": {
    "id": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
    "author": "lemonwang2020 <66710825+lemonwang2020@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Add files via upload",
    "time": 1596468344
  },
  "_maintainer": {
    "name": "Limei Wang",
    "email": "lemon619@gmail.com",
    "login": "lemonwang2020",
    "uuid": 66710825
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "DysPIAData",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.4",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "fastmatch",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "FNN",
      "role": "Imports"
    }
  ],
  "_owner": "lemonwang2020",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "lemonwang2020",
      "count": 2,
      "uuid": 66710825
    }
  ],
  "_userbio": {
    "uuid": 66710825,
    "type": "user",
    "name": "lemonwang2020"
  },
  "_downloads": {
    "count": 242,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DysPIA"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/lemonwang2020/dyspia",
  "_searchresults": 0,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DysPIA.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/lemonwang2020/dyspia",
  "_realowner": "lemonwang2020",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.2",
      "date": "2020-06-24"
    },
    {
      "version": "1.3",
      "date": "2020-07-10"
    }
  ],
  "_exports": [
    "calcDyspiaStat",
    "calcDyspiaStatCumulative",
    "calcDyspiaStatCumulativeBatch",
    "calEdgeCorScore_ESEA",
    "DysGPS",
    "DysPIA",
    "DyspiaSig",
    "DyspiaSimpleImpl",
    "setUpBPPARAM"
  ],
  "_datasets": [
    {
      "name": "class.labels_p53",
      "title": "Example vector of category labels.",
      "object": "class.labels_p53",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "DysGPS_p53",
      "title": "Example vector of DysGPS in p53 data.",
      "object": "DysGPS_p53",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "DyspiaRes_p53",
      "title": "Example list of DysPIA result in p53 data.",
      "object": "DyspiaRes_p53",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "pathway",
        "pval",
        "padj",
        "DysPS",
        "NDysPS",
        "nMoreExtreme",
        "size",
        "leadingEdge"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
    },
    {
      "name": "gene_expression_p53",
      "title": "Example matrix of gene expression value.",
      "object": "gene_expression_p53",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "X786.0",
        "BT.549",
        "CCRF.CEM",
        "COLO.205",
        "EKVX",
        "HCC.2998",
        "HCT.15",
        "HOP.62",
        "HOP.92",
        "HS.578T",
        "HT29",
        "K.562",
        "KM12",
        "M14",
        "MDA.MB.231.ATCC",
        "MDA.MB.435",
        "NCI.H23",
        "NCI.H322M",
        "NCI.H522",
        "OVCAR.3",
        "OVCAR.5",
        "OVCAR.8",
        "PC.3",
        "RXF.393",
        "SF.268",
        "SF.295",
        "SK.MEL.2",
        "SN12C",
        "SNB.19",
        "SNB.75",
        "SW.620",
        "T.47D",
        "U251",
        "A498",
        "A549.ATCC",
        "ACHN",
        "CAKI.1",
        "HCT.116",
        "LOX.IMVI",
        "MALME.3M",
        "MCF7",
        "MOLT.4",
        "NCI.H460",
        "OVCAR.4",
        "SF.539",
        "SK.MEL.5",
        "SR",
        "UACC.257",
        "UACC.62",
        "UO.31"
      ],
      "rows": 6835,
      "table": true,
      "tojson": true
    },
    {
      "name": "sample_background",
      "title": "Example list of gene pair background.",
      "object": "sample_background",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "src",
        "dest"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calcDyspiaStat",
      "title": "calcDyspiaStat: Calculates DysPIA statistics",
      "topics": [
        "calcDyspiaStat"
      ]
    },
    {
      "page": "calcDyspiaStatCumulative",
      "title": "Calculates DysPIA statistic values for all the prefixes of a gene pair set",
      "topics": [
        "calcDyspiaStatCumulative"
      ]
    },
    {
      "page": "calcDyspiaStatCumulativeBatch",
      "title": "Calculates DysPIA statistic values for the gene pair sets",
      "topics": [
        "calcDyspiaStatCumulativeBatch"
      ]
    },
    {
      "page": "calEdgeCorScore_ESEA",
      "title": "calEdgeCorScore_ESE",
      "topics": [
        "calEdgeCorScore_ESEA"
      ]
    },
    {
      "page": "class.labels_p53",
      "title": "Example vector of category labels.",
      "topics": [
        "class.labels_p53"
      ]
    },
    {
      "page": "DysGPS",
      "title": "DysGPS: Calculates Dysregulated gene pair score (DysGPS) for each gene pair",
      "topics": [
        "DysGPS"
      ]
    },
    {
      "page": "DysGPS_p53",
      "title": "Example vector of DysGPS in p53 data.",
      "topics": [
        "DysGPS_p53"
      ]
    },
    {
      "page": "DysPIA",
      "title": "DysPIA: Dysregulated Pathway Identification Analysis",
      "topics": [
        "DysPIA"
      ]
    },
    {
      "page": "DyspiaRes_p53",
      "title": "Example list of DysPIA result in p53 data.",
      "topics": [
        "DyspiaRes_p53"
      ]
    },
    {
      "page": "DyspiaSig",
      "title": "DyspiaSig",
      "topics": [
        "DyspiaSig"
      ]
    },
    {
      "page": "DyspiaSimpleImpl",
      "title": "DyspiaSimpleImpl",
      "topics": [
        "DyspiaSimpleImpl"
      ]
    },
    {
      "page": "gene_expression_p53",
      "title": "Example matrix of gene expression value.",
      "topics": [
        "gene_expression_p53"
      ]
    },
    {
      "page": "sample_background",
      "title": "Example list of gene pair background.",
      "topics": [
        "sample_background"
      ]
    },
    {
      "page": "setUpBPPARAM",
      "title": "setUpBPPARAM",
      "topics": [
        "setUpBPPARAM"
      ]
    }
  ],
  "_readme": "https://github.com/lemonwang2020/dyspia/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "BiocParallel",
    "codetools",
    "cpp11",
    "data.table",
    "DysPIAData",
    "fastmatch",
    "FNN",
    "formatR",
    "futile.logger",
    "futile.options",
    "lambda.r",
    "Rcpp",
    "snow"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "dyspia",
  "_universes": [
    "lemonwang2020"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-05-12T09:18:11.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "508d861c54d742b74b7e66cc8f681302c0d5872150a246b69cd17658ae059586",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-05-12T09:19:07.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "0eea92ecddcaf42d6d5979ba80b15433d974b79a79c8291cc6f426f4db3bed8c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-05-12T09:18:39.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "59985b0e2e87df517d795679641ff154a3e929419e7cc85ea95d64f3e37502ce",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.4",
      "date": "2026-05-12T09:19:01.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "c94e2e9965896b453b9635ea1965293facd5c4a10f9f2cafd820e4f334bf95d1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4",
      "date": "2026-05-12T09:19:27.000Z",
      "arch": "aarch64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "b600a45115a9083ceb870a0f5d1755e6470f324af9667c96d6aeb291d8ff41fa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4",
      "date": "2026-05-12T09:22:41.000Z",
      "arch": "x86_64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "6ced4173481e2bccfef599e9cd81069afddec7fb3024d7c108574f6cbc797b70",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.4",
      "date": "2026-05-12T09:20:53.000Z",
      "arch": "aarch64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "a2e2d7c86b1b144d01c28a4b552af27e101c2b318a341ab5825380a9f8160d34",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.4",
      "date": "2026-05-12T09:24:23.000Z",
      "arch": "x86_64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "8f0f5bc52ec41c57c4e399e0f596ec32bf0410b9d72ab9e9cb13a4188d925544",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.4",
      "date": "2026-05-12T09:17:33.000Z",
      "arch": "x86_64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "1f5438bbb0528f9f606cca2715a5d8ca2d52997d8dfc3cf1f678d57bcd6e7cd8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.4",
      "date": "2026-05-12T09:17:53.000Z",
      "arch": "x86_64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "c10fbc0124fc55ff54a1e27fb9ffe05091374196031725d85bcc16bee8e7c4f6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.4",
      "date": "2026-05-12T09:17:46.000Z",
      "arch": "x86_64",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "efd77ff02da5bcad503b1bc6f2a97929833817bc062551f6800af0543f0732f4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.4",
      "date": "2026-05-22T10:32:56.000Z",
      "arch": "emscripten",
      "commit": "b15711bbb95a2df37d8f44ab81c9fab49b92f61a",
      "fileid": "e1bc7881efe37bc0bcdd2cf1516588206686b33c8acfb3391ba5e4fbcece4f2a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/lemonwang2020/actions/runs/25725012902"
    }
  ]
}