{
  "_id": "6ac21a6e773a0037682c20a1",
  "Package": "FARDEEP",
  "Title": "Fast and Robust Deconvolution of Tumor Infiltrating Lymphocyte\nfrom Expression Profiles using Least Trimmed Squares",
  "Version": "1.0.1",
  "Authors@R": "c(\nperson(\"Yuning\", \"Hao\",  role = c(\"aut\")),\nperson(\"Ming\", \"Yan\",  role = c(\"aut\")),\nperson(\"Blake R.\", \"Heath\",  role = c(\"aut\")),\nperson(\"Yu L.\", \"Lei\",  role = c(\"aut\")),\nperson(\"Yuying\", \"Xie\", email = \"xyy@egr.msu.edu\",\nrole = c(\"aut\",\"cre\")))",
  "Description": "Using the idea of least trimmed square, it could\nautomatically detects and removes outliers from data before\nestimating the coefficients. It is a robust machine learning\ntool which can be applied to gene-expression deconvolution\ntechnique. Yuning Hao, Ming Yan, Blake R. Heath, Yu L. Lei and\nYuying Xie (2019) <doi:10.1101/358366>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "6.1.1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-04 09:14:28 UTC",
    "User": "root"
  },
  "Author": "Yuning Hao [aut], Ming Yan [aut], Blake R. Heath [aut], Yu L.\nLei [aut], Yuying Xie [aut, cre]",
  "Maintainer": "Yuying Xie <xyy@egr.msu.edu>",
  "Repository": "https://yuyingxie.r-universe.dev",
  "Date/Publication": "2019-04-24 14:10:03 UTC",
  "RemoteUrl": "https://github.com/cran/FARDEEP",
  "RemoteRef": "HEAD",
  "RemoteSha": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
  "_user": "yuyingxie",
  "_type": "src",
  "_file": "FARDEEP_1.0.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/1f605bd9e64ee4b572c86e09de8a6f4ae0017290c3eb1970ad450e5b7e9c8f3b",
  "_filesize": 2345579,
  "_sha256": "1f605bd9e64ee4b572c86e09de8a6f4ae0017290c3eb1970ad450e5b7e9c8f3b",
  "_expires": "2027-01-12T09:20:44.000Z",
  "_created": "2026-10-04T09:14:28.000Z",
  "_published": "2026-10-04T09:20:46.462Z",
  "_jobs": [
    {
      "job": 111404534645,
      "time": 94,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11299600867"
    },
    {
      "job": 111404534648,
      "time": 87,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11299311719"
    },
    {
      "job": 111404534631,
      "time": 190,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11299680157"
    },
    {
      "job": 111404534692,
      "time": 144,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11299062161"
    },
    {
      "job": 111404015495,
      "time": 193,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11299142864"
    },
    {
      "job": 111404534654,
      "time": 87,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11298852247"
    },
    {
      "job": 111404534748,
      "time": 52,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11299087960"
    },
    {
      "job": 111404534704,
      "time": 52,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11299507091"
    },
    {
      "job": 111404534672,
      "time": 53,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11299212836"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/37191332261",
  "_status": "success",
  "_upstream": "https://github.com/cran/FARDEEP",
  "_commit": {
    "id": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
    "author": "Yuying Xie <xyy@egr.msu.edu>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.1\n",
    "time": 1556115003
  },
  "_maintainer": {
    "name": "Yuying Xie",
    "email": "xyy@egr.msu.edu",
    "login": "yuyingxie",
    "description": "CMSE\nMichigan State University",
    "uuid": 7158255
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3.0",
      "role": "Depends"
    },
    {
      "package": "nnls",
      "version": ">= 1.4",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "role": "Imports"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "yuyingxie",
      "count": 1,
      "uuid": 7158255
    }
  ],
  "_userbio": {
    "uuid": 7158255,
    "type": "user",
    "name": "Yuying Xie",
    "followers": 2,
    "description": "CMSE\r\nMichigan State University"
  },
  "_downloads": {
    "count": 369,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FARDEEP"
  },
  "_mentions": 5,
  "_searchresults": 50,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/FARDEEP.html",
    "extra/manual.pdf",
    "LICENSE"
  ],
  "_realowner": "yuyingxie",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2019-04-24"
    }
  ],
  "_exports": [
    "alts",
    "fardeep",
    "sample.sim",
    "tuningBIC"
  ],
  "_datasets": [
    {
      "name": "LM22",
      "title": "Siganature matrix",
      "object": "LM22",
      "class": [
        "data.frame"
      ],
      "fields": [
        "B.cells.naive",
        "B.cells.memory",
        "Plasma.cells",
        "T.cells.CD8",
        "T.cells.CD4.naive",
        "T.cells.CD4.memory.resting",
        "T.cells.CD4.memory.activated",
        "T.cells.follicular.helper",
        "T.cells.regulatory.Tregs.",
        "T.cells.gamma.delta",
        "NK.cells.resting",
        "NK.cells.activated",
        "Monocytes",
        "Macrophages.M0",
        "Macrophages.M1",
        "Macrophages.M2",
        "Dendritic.cells.resting",
        "Dendritic.cells.activated",
        "Mast.cells.resting",
        "Mast.cells.activated",
        "Eosinophils",
        "Neutrophils"
      ],
      "rows": 547,
      "table": true,
      "tojson": true
    },
    {
      "name": "mixture",
      "title": "Gene-expression data from 14 follicular lymphoma patients",
      "object": "mixture",
      "class": [
        "data.frame"
      ],
      "fields": [
        "GSM1587831",
        "GSM1587832",
        "GSM1587833",
        "GSM1587834",
        "GSM1587835",
        "GSM1587836",
        "GSM1587837",
        "GSM1587838",
        "GSM1587839",
        "GSM1587840",
        "GSM1587841",
        "GSM1587842",
        "GSM1587843",
        "GSM1587844"
      ],
      "rows": 19416,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "alts",
      "title": "Using the basic idea of least trimmed square to detect and remove outliers before estimating the coefficients. Adaptive least trimmed square.",
      "topics": [
        "alts"
      ]
    },
    {
      "page": "fardeep",
      "title": "Using the idea of least trimmed square to detect and remove outliers before estimating the coefficients. A robust method for gene-expression deconvolution.",
      "topics": [
        "fardeep"
      ]
    },
    {
      "page": "LM22",
      "title": "Siganature matrix",
      "topics": [
        "LM22"
      ]
    },
    {
      "page": "mixture",
      "title": "Gene-expression data from 14 follicular lymphoma patients",
      "topics": [
        "mixture"
      ]
    },
    {
      "page": "sample.sim",
      "title": "Generate random sample with different proportion of outliers and leverage points",
      "topics": [
        "sample.sim"
      ]
    },
    {
      "page": "tuningBIC",
      "title": "Tuning parameter k in function alts using Bayesian Information Criterion (BIC) with some adjustment.",
      "topics": [
        "tuningBIC"
      ]
    }
  ],
  "_rundeps": [
    "nnls",
    "preprocessCore"
  ],
  "_score": 2.8750612633917,
  "_indexed": true,
  "_nocasepkg": "fardeep",
  "_universes": [
    "yuyingxie"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-10-04T09:16:05.000Z",
      "distro": "resolute",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "https://r2.ropensci.org/e467cc2dd5ba19f581e829d5af958a7a54f7125b87f9b8783b3b555d2b4a1c88",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/37191332261"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-10-04T09:15:58.000Z",
      "distro": "resolute",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "https://r2.ropensci.org/24fd181b787fd7598cd9dccb2d4d5b7b5f2ba89feede26201d137c1f4a657946",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/37191332261"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-10-04T09:19:20.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "https://r2.ropensci.org/a29d122ab345823abe3792ccc99ac635f4f25a0a2cbc463afa7e53db09fc38dd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/37191332261"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-10-04T09:19:42.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "https://r2.ropensci.org/9c1ce8214b2cc0905685d40ddc52cb162ea1b8a77a2d2764b0f41a6a155e83a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/37191332261"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.1",
      "date": "2026-10-04T09:16:07.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "https://r2.ropensci.org/cec7bed478a3ddfe8673cd3af14c8debf9b3741156cc3b4eafc8235d7fa798b0",
      "status": "success",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/37191332261"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-10-04T09:15:18.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "https://r2.ropensci.org/8e6452bb07372c05a57b2eb625f53e1501dea4400f7c19074bd637b957be1dee",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/37191332261"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-10-04T09:15:19.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "https://r2.ropensci.org/948f25f1f13478515fe2f0698a2b7e9cfcd7703211c075e92746ac2a2a116a34",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/37191332261"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-10-04T09:15:20.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "https://r2.ropensci.org/9276267a01c901f25169eacc14c1d351bd333252bc0d8f3e283a317156cdfe66",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/37191332261"
    }
  ]
}