{
  "_id": "6a1afe5c1d7bb097a09fe5cd",
  "Package": "DeconRNASeq",
  "Type": "Package",
  "Title": "Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data",
  "Version": "1.54.0",
  "Date": "2013-01-22",
  "Author": "Ting Gong <tinggong@gmail.com> Joseph D. Szustakowski\n<joseph.szustakowski@novartis.com>",
  "Maintainer": "Ting Gong <tinggong@gmail.com>",
  "Description": "DeconSeq is an R package for deconvolution of\nheterogeneous tissues based on mRNA-Seq data. It modeled\nexpression levels from heterogeneous cell populations in\nmRNA-Seq as the weighted average of expression from different\nconstituting cell types and predicted cell type proportions of\nsingle expression profiles.",
  "License": "GPL-2",
  "Packaged": {
    "Date": "2026-05-30 09:59:50 UTC",
    "User": "root"
  },
  "biocViews": "DifferentialExpression",
  "PackageStatus": "Deprecated",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:53 UTC",
  "RemoteUrl": "https://github.com/bioc/DeconRNASeq",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "473698cc2bba2253d5e17d91952b34c0f0abcdfe",
  "NeedsCompilation": "no",
  "MD5sum": "1715981b9c232924000ec35b66934e1b",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "DeconRNASeq_1.54.0.tar.gz",
  "_fileid": "1c14ef9f6bac2891e1cb0da1ca215e0fe97d38eebed775c776f0d57a0e79a66f",
  "_filesize": 6877334,
  "_sha256": "1c14ef9f6bac2891e1cb0da1ca215e0fe97d38eebed775c776f0d57a0e79a66f",
  "_created": "2026-05-30T09:59:50.000Z",
  "_published": "2026-05-30T15:12:28.568Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78641245970,
      "time": 137,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "FAILURE",
      "artifact": ""
    },
    {
      "job": 78641245979,
      "time": 131,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307610959"
    },
    {
      "job": 78641245976,
      "time": 144,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307612198"
    },
    {
      "job": 78641245994,
      "time": 105,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7309145888"
    },
    {
      "job": 78641245987,
      "time": 99,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7309144601"
    },
    {
      "job": 78640248100,
      "time": 164,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307363098"
    },
    {
      "job": 78641245974,
      "time": 102,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307608327"
    },
    {
      "job": 78641245993,
      "time": 83,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307607505"
    },
    {
      "job": 78641246011,
      "time": 82,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307607312"
    },
    {
      "job": 78641246003,
      "time": 72,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307606438"
    }
  ],
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680305955",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/DeconRNASeq",
  "_commit": {
    "id": "473698cc2bba2253d5e17d91952b34c0f0abcdfe",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379813
  },
  "_maintainer": {
    "name": "Ting Gong",
    "email": "tinggong@gmail.com",
    "login": "tinggong1",
    "description": "",
    "uuid": 94084015
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.14.0",
      "role": "Depends"
    },
    {
      "package": "limSolve",
      "role": "Depends"
    },
    {
      "package": "pcaMethods",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Depends"
    },
    {
      "package": "grid",
      "role": "Depends"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-11",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "differentialexpression"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 790,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DeconRNASeq"
  },
  "_mentions": 23,
  "_searchresults": 89,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DeconRNASeq.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "condplot",
    "decon.bootstrap",
    "DeconRNASeq",
    "multiplot",
    "rmse"
  ],
  "_datasets": [
    {
      "name": "datasets",
      "title": "data objects for liver and kidney mixing samples",
      "object": "liver_kidney_ascii",
      "file": "liver_kidney_ascii.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "reads.1",
        "reads.2",
        "reads.3",
        "reads.4",
        "reads.5",
        "reads.6",
        "reads.7"
      ],
      "rows": 31979,
      "table": true,
      "tojson": true
    },
    {
      "name": "datasets",
      "title": "data objects for liver and kidney mixing samples",
      "object": "liver_kidney",
      "file": "liver_kidney.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "reads.1",
        "reads.2",
        "reads.3",
        "reads.4",
        "reads.5",
        "reads.6",
        "reads.7"
      ],
      "rows": 31979,
      "table": true,
      "tojson": true
    },
    {
      "name": "fraction",
      "title": "mixing fractions for multi-tissues mixing samples",
      "object": "multi_tissue",
      "file": "multi_tissue.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "brain",
        "muscle",
        "lung",
        "liver",
        "heart"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "proportions",
      "title": "proportions for liver and kidney mixing samples",
      "object": "liver_kidney_ascii",
      "file": "liver_kidney_ascii.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "liver",
        "kidney"
      ],
      "rows": 7,
      "table": true,
      "tojson": true
    },
    {
      "name": "proportions",
      "title": "proportions for liver and kidney mixing samples",
      "object": "liver_kidney",
      "file": "liver_kidney.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "liver",
        "kidney"
      ],
      "rows": 7,
      "table": true,
      "tojson": true
    },
    {
      "name": "signatures",
      "title": "data objects for liver and kidney pure samples",
      "object": "liver_kidney_ascii",
      "file": "liver_kidney_ascii.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "kidney",
        "liver"
      ],
      "rows": 630,
      "table": true,
      "tojson": true
    },
    {
      "name": "signatures",
      "title": "data objects for liver and kidney pure samples",
      "object": "liver_kidney",
      "file": "liver_kidney.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "kidney",
        "liver"
      ],
      "rows": 630,
      "table": true,
      "tojson": true
    },
    {
      "name": "x.data",
      "title": "data objects for multi-tissues mixing samples",
      "object": "multi_tissue",
      "file": "multi_tissue.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "genes.with.val",
        "reads.1.RPKM",
        "reads.2.RPKM",
        "reads.3.RPKM",
        "reads.4.RPKM",
        "reads.5.RPKM",
        "reads.6.RPKM",
        "reads.7.RPKM",
        "reads.8.RPKM",
        "reads.9.RPKM",
        "reads.10.RPKM"
      ],
      "rows": 28745,
      "table": true,
      "tojson": true
    },
    {
      "name": "x.signature",
      "title": "data objects for multi-tissues pure samples",
      "object": "multi_tissue",
      "file": "multi_tissue.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "genes.diff",
        "brain",
        "muscle",
        "lung",
        "liver",
        "heart",
        "p_val.filtered.diff"
      ],
      "rows": 26385,
      "table": true,
      "tojson": true
    },
    {
      "name": "x.signature.filtered",
      "title": "filtered signatures for multi-tissues pure samples",
      "object": "multi_tissue",
      "file": "multi_tissue.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "genes.diff",
        "brain",
        "muscle",
        "lung",
        "liver",
        "heart",
        "p_val.filtered.diff"
      ],
      "rows": 25861,
      "table": true,
      "tojson": true
    },
    {
      "name": "x.signature.filtered.optimal",
      "title": "selected signatures from multi-tissues pure samples",
      "object": "multi_tissue",
      "file": "multi_tissue.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "genes.diff",
        "brain",
        "muscle",
        "lung",
        "liver",
        "heart",
        "p_val.filtered.diff"
      ],
      "rows": 1570,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "DeconRNASeq-package",
      "title": "package DeconRNASeq contains function \"DeconRNASeq\", implementing the decomposition of RNA-Seq expression profilings of heterogeneous tissues into cell/tissue type specific expression and cell type concentration based on cell-type-specific reference measurements.",
      "topics": [
        "DeconRNASeq.package",
        "DeconRNASeq_package"
      ]
    },
    {
      "page": "all.datasets",
      "title": "data objects for rat liver_brain samples",
      "topics": [
        "all.datasets"
      ]
    },
    {
      "page": "array.proportions",
      "title": "proportions for rat liver and brain mixing samples",
      "topics": [
        "array.proportions"
      ]
    },
    {
      "page": "array.signatures",
      "title": "data objects for rat liver and brain pure samples",
      "topics": [
        "array.signatures"
      ]
    },
    {
      "page": "condplot",
      "title": "Draw the plot of the condition numbers vs. the number of genes in the signature matrix",
      "topics": [
        "condplot"
      ]
    },
    {
      "page": "datasets",
      "title": "data objects for liver and kidney mixing samples",
      "topics": [
        "datasets"
      ]
    },
    {
      "page": "decon.bootstrap",
      "title": "Estimate the confidence interval for the proportions predicted by deconvolution",
      "topics": [
        "decon.bootstrap"
      ]
    },
    {
      "page": "DeconRNASeq",
      "title": "Function for Deconvolution of Complex Samples from RNA-Seq.",
      "topics": [
        "DeconRNASeq"
      ]
    },
    {
      "page": "fraction",
      "title": "mixing fractions for multi-tissues mixing samples",
      "topics": [
        "fraction"
      ]
    },
    {
      "page": "liver_kidney",
      "title": "data objects for liver and kidney mixing samples",
      "topics": [
        "liver_kidney"
      ]
    },
    {
      "page": "multi_tissue",
      "title": "data objects for multi-tissues mixing samples",
      "topics": [
        "multi_tissue"
      ]
    },
    {
      "page": "multiplot",
      "title": "Draw the plots of proportions of cells determined from deconvolution vs. proportions of the cells actually mixed (when available) with RMSE.",
      "topics": [
        "multiplot"
      ]
    },
    {
      "page": "proportions",
      "title": "proportions for liver and kidney mixing samples",
      "topics": [
        "proportions"
      ]
    },
    {
      "page": "rmse",
      "title": "Calculate the differences between proportions predicted by deconvolution and the values actually measured",
      "topics": [
        "rmse"
      ]
    },
    {
      "page": "signatures",
      "title": "data objects for liver and kidney pure samples",
      "topics": [
        "signatures"
      ]
    },
    {
      "page": "x.data",
      "title": "data objects for multi-tissues mixing samples",
      "topics": [
        "x.data"
      ]
    },
    {
      "page": "x.signature",
      "title": "data objects for multi-tissues pure samples",
      "topics": [
        "x.signature"
      ]
    },
    {
      "page": "x.signature.filtered",
      "title": "filtered signatures for multi-tissues pure samples",
      "topics": [
        "x.signature.filtered"
      ]
    },
    {
      "page": "x.signature.filtered.optimal",
      "title": "selected signatures from multi-tissues pure samples",
      "topics": [
        "x.signature.filtered.optimal"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "cli",
    "cpp11",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "limSolve",
    "lpSolve",
    "MASS",
    "pcaMethods",
    "quadprog",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 3.4265112613645754,
  "_indexed": false,
  "_nocasepkg": "deconrnaseq",
  "_universes": [
    "bioc-release"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.54.0",
      "date": "2026-05-30T10:45:00.000Z",
      "distro": "noble",
      "commit": "473698cc2bba2253d5e17d91952b34c0f0abcdfe",
      "fileid": "b288f7feacddf8169d73f237748ce4825c7bff3fb739ca43e7589418f26bf46a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680305955"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.54.0",
      "date": "2026-05-30T10:45:15.000Z",
      "distro": "noble",
      "commit": "473698cc2bba2253d5e17d91952b34c0f0abcdfe",
      "fileid": "2f5643072105d6afae2e2fb790752f64cdf06a3dd1882da613c4f5beaf70644c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680305955"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.54.0",
      "date": "2026-05-30T15:11:40.000Z",
      "commit": "473698cc2bba2253d5e17d91952b34c0f0abcdfe",
      "fileid": "b0c76c998d071664576eb4dfb9cb3075a0d36a2105c9b86911e59b40bae0edf6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680305955"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.54.0",
      "date": "2026-05-30T15:11:30.000Z",
      "commit": "473698cc2bba2253d5e17d91952b34c0f0abcdfe",
      "fileid": "7accdf66f72c3c149f31274421304796e4b462cae84bded79d467c719f73d2dc",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680305955"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.54.0",
      "date": "2026-05-30T10:44:54.000Z",
      "commit": "473698cc2bba2253d5e17d91952b34c0f0abcdfe",
      "fileid": "c54dfd07b2afaea908c4138427d1541fa1523bf70643f102546ae93d620874aa",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680305955"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.54.0",
      "date": "2026-05-30T10:44:18.000Z",
      "commit": "473698cc2bba2253d5e17d91952b34c0f0abcdfe",
      "fileid": "f19dc52141e4399750dda59af990076f5ecbb73f236ec194307145b7e8040fc3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680305955"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.54.0",
      "date": "2026-05-30T10:44:17.000Z",
      "commit": "473698cc2bba2253d5e17d91952b34c0f0abcdfe",
      "fileid": "23e89eff15b75dd7dfd916cc4d87713dffcad1636ff48b89aceed88ca6b0bb36",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680305955"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.54.0",
      "date": "2026-05-30T10:44:08.000Z",
      "commit": "473698cc2bba2253d5e17d91952b34c0f0abcdfe",
      "fileid": "59e6739d79398b2a27683028fc32000174b05809dd4824063e11eeba24f0dfbf",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680305955"
    }
  ]
}