{
  "_id": "6a23e9a6a1338011a79ebebe",
  "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": "2026-06-06 09:31:40 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",
  "MD5sum": "2d44cf5d15eab6c8f7a012c9f8f96de8",
  "_user": "yuyingxie",
  "_type": "src",
  "_file": "FARDEEP_1.0.1.tar.gz",
  "_fileid": "a730c04fa7b6faf31dc749f08fd155d98fa5555a01e659141350bed865cf501b",
  "_filesize": 2344523,
  "_sha256": "a730c04fa7b6faf31dc749f08fd155d98fa5555a01e659141350bed865cf501b",
  "_created": "2026-06-06T09:31:40.000Z",
  "_published": "2026-06-06T09:34:30.532Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79867750116,
      "time": 97,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7453279205"
    },
    {
      "job": 79867750121,
      "time": 96,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7453278924"
    },
    {
      "job": 79867750114,
      "time": 140,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7453280709"
    },
    {
      "job": 79867750109,
      "time": 120,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7453279221"
    },
    {
      "job": 79867616639,
      "time": 141,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7453268525"
    },
    {
      "job": 79867750108,
      "time": 87,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7453278108"
    },
    {
      "job": 79867750122,
      "time": 71,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7453276184"
    },
    {
      "job": 79867750123,
      "time": 65,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7453275629"
    },
    {
      "job": 79867750125,
      "time": 75,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7453276909"
    }
  ],
  "_buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/27058685792",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_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
  },
  "_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": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "yuyingxie",
      "count": 1,
      "uuid": 7158255
    }
  ],
  "_userbio": {
    "uuid": 7158255,
    "type": "user",
    "name": "Yuying Xie",
    "description": "CMSE\r\nMichigan State University"
  },
  "_downloads": {
    "count": 206,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FARDEEP"
  },
  "_searchresults": 57,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/FARDEEP.html",
    "manual.pdf"
  ],
  "_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": 1.7558748556724915,
  "_indexed": true,
  "_nocasepkg": "fardeep",
  "_universes": [
    "yuyingxie"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-06T09:33:24.000Z",
      "distro": "noble",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "7f9561278916e2e4a4113efb6a391b9ecfac47a0d6c1dc0f67c0a2fb5c8e539a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/27058685792"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-06T09:33:23.000Z",
      "distro": "noble",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "34edf4bb9ca4055f0117bc0bf7acc3c86c4c068cb09c8bfe8a4f36a0bf279079",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/27058685792"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-06T09:33:42.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "7f5b2436dc8773c1e9e00b2f3dd8bb5c126e8c151e76f132ed14aab129d1802f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/27058685792"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-06T09:33:27.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "69e93d8771a9504ff1132d254e877e1badeefee6658ff71ad94427f1df9a5109",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/27058685792"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.1",
      "date": "2026-06-06T09:33:25.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "db01cf550cbe39fe3ef28636891fa227fdca767549422e54237633e926283b03",
      "status": "success",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/27058685792"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-06T09:32:52.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "bc7bda4c50f8ead74ba39bcb2ee0a536cb480b49a45d3767bc8b335a72194b10",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/27058685792"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-06T09:32:48.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "858c82776e677f15384e93be23b0c17744e5fd8c438850c21ee7a66bc5480828",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/27058685792"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-06T09:33:00.000Z",
      "commit": "a35a92fe91112df4fbbaa70c390dbf9208252ec3",
      "fileid": "17a97e5154e9dc553569d03efdfd1f74c205eb4b883d00e544bba04d75f2f44c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/yuyingxie/actions/runs/27058685792"
    }
  ]
}