{
  "_id": "6a1af46d1d7bb097a09f8cac",
  "Package": "sigsquared",
  "Type": "Package",
  "Title": "Gene signature generation for functionally validated signaling\npathways",
  "Version": "1.45.0",
  "Date": "2015-01-23",
  "Author": "UnJin Lee",
  "Maintainer": "UnJin Lee <unjin@uchicago.edu>",
  "Description": "By leveraging statistical properties (log-rank test for\nsurvival) of patient cohorts defined by binary thresholds,\npoor-prognosis patients are identified by the sigsquared\npackage via optimization over a cost function reducing type I\nand II error.",
  "biocViews": "",
  "License": "GPL version 3",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:40:38 UTC",
  "RemoteUrl": "https://github.com/bioc/sigsquared",
  "RemoteRef": "HEAD",
  "RemoteSha": "37ea3e2fe0cc90f76f41646f146d6078c2f4b92b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:46:04 UTC",
    "User": "root"
  },
  "MD5sum": "da67b3ba0b4be9761475b9b540b1b152",
  "_user": "bioc",
  "_type": "src",
  "_file": "sigsquared_1.45.0.tar.gz",
  "_fileid": "9357ff06996bc2086b31fd17dea66367b2bb40cfd3dea6cea1b6847289d97df1",
  "_filesize": 448464,
  "_sha256": "9357ff06996bc2086b31fd17dea66367b2bb40cfd3dea6cea1b6847289d97df1",
  "_created": "2026-05-30T09:46:04.000Z",
  "_published": "2026-05-30T14:30:05.561Z",
  "_jobs": [
    {
      "job": 78640569008,
      "time": 129,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307467951"
    },
    {
      "job": 78640569016,
      "time": 172,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307470463"
    },
    {
      "job": 78640569014,
      "time": 164,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307469704"
    },
    {
      "job": 78640569011,
      "time": 91,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308874018"
    },
    {
      "job": 78640569027,
      "time": 119,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308877230"
    },
    {
      "job": 78639916496,
      "time": 174,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307283827"
    },
    {
      "job": 78640568987,
      "time": 91,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307463265"
    },
    {
      "job": 78640569053,
      "time": 102,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307464818"
    },
    {
      "job": 78640569052,
      "time": 90,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307463815"
    },
    {
      "job": 78640569033,
      "time": 91,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307463894"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 5,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677016783",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/sigsquared",
  "_commit": {
    "id": "37ea3e2fe0cc90f76f41646f146d6078c2f4b92b",
    "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": 1777380038
  },
  "_maintainer": {
    "name": "UnJin Lee",
    "email": "unjin@uchicago.edu",
    "login": "avianalter",
    "description": "",
    "uuid": 9277890
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.2.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.45.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.44.0",
      "bioc": "3.23"
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 380,
    "source": "https://www.bioconductor.org/packages/stats/bioc/sigsquared"
  },
  "_searchresults": 1,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/sigsquared.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "analysisPipeline",
    "ensembleAdjustable",
    "getDirect",
    "getGenes",
    "getNGenes",
    "getThresholds",
    "setDirect",
    "setGenes",
    "setGeneSignature",
    "setThresholds"
  ],
  "_datasets": [
    {
      "name": "BrCa443",
      "title": "Breast Cancer 443 Data Set",
      "object": "BrCa443",
      "file": "BrCa443.RData",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "analysisPipeline",
      "title": "Training of thresholds",
      "topics": [
        "analysisPipeline"
      ]
    },
    {
      "page": "BrCa443",
      "title": "Breast Cancer 443 Data Set",
      "topics": [
        "BrCa443"
      ]
    },
    {
      "page": "ensembleAdjustable",
      "title": "Application of geneSignature object",
      "topics": [
        "ensembleAdjustable"
      ]
    },
    {
      "page": "geneSignature-class",
      "title": "Class '\"geneSignature\"'",
      "topics": [
        "analysisPipeline,ExpressionSet,geneSignature-method",
        "ensembleAdjustable,ExpressionSet,geneSignature-method",
        "ensembleAdjustable,matrix,geneSignature-method",
        "geneSignature-class",
        "getDirect,geneSignature-method",
        "getGenes,geneSignature-method",
        "getGenes,solnSpace-method",
        "getNGenes,geneSignature-method",
        "getThresholds,geneSignature-method",
        "getThresholds,solnSpace-method",
        "setDirect,geneSignature,numeric-method",
        "setGenes,geneSignature-method",
        "setGenes,solnSpace-method",
        "setGeneSignature,geneSignature-method",
        "setThresholds,geneSignature-method",
        "setThresholds,solnSpace-method"
      ]
    },
    {
      "page": "setGeneSignature",
      "title": "geneSignature functions",
      "topics": [
        "getDirect",
        "getGenes",
        "getNGenes",
        "getThresholds",
        "setDirect",
        "setGenes",
        "setGeneSignature",
        "setThresholds"
      ]
    },
    {
      "page": "sigsquared",
      "title": "The sigsquared package",
      "topics": [
        "sigsquared"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "generics",
    "lattice",
    "Matrix",
    "survival"
  ],
  "_vignettes": [
    {
      "source": "sigsquared.Rnw",
      "filename": "sigsquared.pdf",
      "title": "SigSquared",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2015-02-28 00:43:36",
      "modified": "2015-02-28 00:43:36",
      "commits": 1
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "sigsquared",
  "_universes": [
    "bioc",
    "avianalter"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.45.0",
      "date": "2026-05-30T10:19:05.000Z",
      "distro": "noble",
      "commit": "37ea3e2fe0cc90f76f41646f146d6078c2f4b92b",
      "fileid": "f4a79903a1c51cc57925b61f91229a57c74d9db56c760ff77af9bdd89282c0c4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677016783"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.45.0",
      "date": "2026-05-30T10:18:52.000Z",
      "distro": "noble",
      "commit": "37ea3e2fe0cc90f76f41646f146d6078c2f4b92b",
      "fileid": "a8b64c5c8cc4e92aafbc2a47f75a1fc2c1334637093d4998d275c5008230c866",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677016783"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.45.0",
      "date": "2026-05-30T14:28:56.000Z",
      "commit": "37ea3e2fe0cc90f76f41646f146d6078c2f4b92b",
      "fileid": "0c74ab499120c465cfc13ba76cd9b0fa0af9e5b2801179529e32e97753a1e67c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677016783"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.45.0",
      "date": "2026-05-30T14:29:20.000Z",
      "commit": "37ea3e2fe0cc90f76f41646f146d6078c2f4b92b",
      "fileid": "a0a37fab2490daa4842e956b6a1b3ac21fb6cd87d1e72317fd727bd6fa54b360",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677016783"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.45.0",
      "date": "2026-05-30T10:18:21.000Z",
      "commit": "37ea3e2fe0cc90f76f41646f146d6078c2f4b92b",
      "fileid": "41eca4f0234fad3868208ff887e8977616771a158738d89c182d2f5ed6e50573",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677016783"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-05-30T10:17:53.000Z",
      "commit": "37ea3e2fe0cc90f76f41646f146d6078c2f4b92b",
      "fileid": "31f9ebf35eb961f739170460ed5c2be6429ea4d33fb17a5c9bd5e22184b9b48d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677016783"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-05-30T10:17:42.000Z",
      "commit": "37ea3e2fe0cc90f76f41646f146d6078c2f4b92b",
      "fileid": "02479cd614be292afbccd808d6d869e2ae144ecc4dbbef827ea6e65a2c92a703",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677016783"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-05-30T10:17:47.000Z",
      "commit": "37ea3e2fe0cc90f76f41646f146d6078c2f4b92b",
      "fileid": "6f02bbdbff880a29fee6a6ea8a95218d0800d5d8258bfafff55b2f11a8b390a5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677016783"
    }
  ]
}