{
  "_id": "6a1042e2acfb0bcc41c9dd18",
  "Package": "BRETIGEA",
  "Title": "Brain Cell Type Specific Gene Expression Analysis",
  "Version": "1.0.4",
  "Author": "Andrew McKenzie [aut, cre], Minghui Wang [aut], Bin Zhang [aut]",
  "Maintainer": "Andrew McKenzie <amckenz@gmail.com>",
  "Description": "Analysis of relative cell type proportions in bulk gene\nexpression data. Provides a well-validated set of brain cell\ntype-specific marker genes derived from multiple types of\nexperiments, as described in McKenzie (2018)\n<doi:10.1038/s41598-018-27293-5>. For brain tissue data sets,\nthere are marker genes available for astrocytes, endothelial\ncells, microglia, neurons, oligodendrocytes, and\noligodendrocyte precursor cells, derived from each of human,\nmice, and combination human/mouse data sets. However, if you\nhave access to your own marker genes, the functions can be\napplied to bulk gene expression data from any tissue. Also\nimplements multiple options for relative cell type proportion\nestimation using these marker genes, adapting and expanding on\napproaches from the 'CellCODE' R package described in Chikina\n(2015) <doi:10.1093/bioinformatics/btv015>. The number of cell\ntype marker genes used in a given analysis can be increased or\ndecreased based on your preferences and the data set. Finally,\nprovides functions to use the estimates to adjust for\nvariability in the relative proportion of cell types across\nsamples prior to downstream analyses.",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.2.3",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Repository": "https://andymckenzie.r-universe.dev",
  "Date/Publication": "2023-12-27 21:25:10 UTC",
  "RemoteUrl": "https://github.com/andymckenzie/bretigea",
  "RemoteRef": "HEAD",
  "RemoteSha": "b93da3fd0e7d76ccc4b58037024d17dfd3e1cfa7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-11 07:10:54 UTC",
    "User": "root"
  },
  "MD5sum": "15bf6b9a179da6fd02570c005ace1c36",
  "_user": "andymckenzie",
  "_type": "src",
  "_file": "BRETIGEA_1.0.4.tar.gz",
  "_fileid": "3e59d42c4bd575493664a7f49ae47052775c585484096477030fc5c6d22caa31",
  "_filesize": 1490681,
  "_sha256": "3e59d42c4bd575493664a7f49ae47052775c585484096477030fc5c6d22caa31",
  "_created": "2026-05-11T07:10:54.000Z",
  "_published": "2026-05-22T11:49:54.401Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77373631954,
      "time": 153,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6912341775"
    },
    {
      "job": 77373632022,
      "time": 124,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6912333227"
    },
    {
      "job": 77373631919,
      "time": 91,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6912323885"
    },
    {
      "job": 77373632158,
      "time": 121,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6912332625"
    },
    {
      "job": 77373631693,
      "time": 233,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6912299163"
    },
    {
      "job": 77373631714,
      "time": 102,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7159774253"
    },
    {
      "job": 77373631892,
      "time": 96,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6912326096"
    },
    {
      "job": 77373632163,
      "time": 92,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6912326728"
    },
    {
      "job": 77373632041,
      "time": 149,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6912341451"
    }
  ],
  "_buildurl": "https://github.com/r-universe/andymckenzie/actions/runs/25655533729",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/andymckenzie/bretigea",
  "_commit": {
    "id": "b93da3fd0e7d76ccc4b58037024d17dfd3e1cfa7",
    "author": "brainpreservation <98316871+brainpreservation@users.noreply.github.com>",
    "committer": "brainpreservation <98316871+brainpreservation@users.noreply.github.com>",
    "message": "spelling\n",
    "time": 1703712310
  },
  "_maintainer": {
    "name": "Andrew McKenzie",
    "email": "amckenz@gmail.com",
    "login": "andymckenzie",
    "uuid": 1280394
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "stats",
      "role": "Suggests"
    },
    {
      "package": "utils",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "andymckenzie",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "cell-type",
    "gene-expression",
    "gene-expression-signatures"
  ],
  "_stars": 17,
  "_contributors": [
    {
      "user": "andymckenzie",
      "count": 25,
      "uuid": 1280394
    },
    {
      "user": "brainpreservation",
      "count": 3,
      "uuid": 98316871
    }
  ],
  "_userbio": {
    "uuid": 1280394,
    "type": "user",
    "name": "Andy McKenzie"
  },
  "_downloads": {
    "count": 258,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BRETIGEA"
  },
  "_mentions": 7,
  "_devurl": "https://github.com/andymckenzie/bretigea",
  "_searchresults": 44,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BRETIGEA.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/andymckenzie/bretigea",
  "_realowner": "andymckenzie",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2018-09-30"
    },
    {
      "version": "1.0.3",
      "date": "2021-05-05"
    }
  ],
  "_exports": [
    "adjustBrainCells",
    "adjustCells",
    "brainCells",
    "findCells"
  ],
  "_datasets": [
    {
      "name": "aba_marker_expression",
      "title": "Normalized FPKM expression data from a subset of the Allen Brain Atlas Aging, Dementia, and TBI study.",
      "object": "aba_marker_expression",
      "class": [
        "data.frame"
      ],
      "fields": [
        "X488395315",
        "X496100277",
        "X496100278",
        "X496100279",
        "X496100281",
        "X496100283",
        "X496100284",
        "X496100285",
        "X496100287",
        "X496100288",
        "X496100290",
        "X496100291",
        "X496100292",
        "X496100294",
        "X496100295",
        "X496100296",
        "X496100297",
        "X496100301",
        "X496100303",
        "X496100304",
        "X496100305",
        "X496100306",
        "X496100307",
        "X496100310",
        "X496100312",
        "X496100313",
        "X496100314",
        "X496100315",
        "X496100316",
        "X496100317",
        "X496100318",
        "X496100319",
        "X496100320",
        "X496100321",
        "X496100322",
        "X496100323",
        "X496100324",
        "X496100326",
        "X496100327",
        "X496100328",
        "X496100329",
        "X496100330",
        "X496100331",
        "X496100332",
        "X496100333",
        "X496100334",
        "X496100335",
        "X496100336",
        "X496100337",
        "X496100338",
        "X496100339",
        "X496100340",
        "X496100341",
        "X496100342",
        "X496100343",
        "X496100344",
        "X496100345",
        "X496100346",
        "X496100347",
        "X496100348",
        "X496100349",
        "X496100350",
        "X496100351",
        "X496100352",
        "X496100353",
        "X496100354",
        "X496100355",
        "X496100356",
        "X496100357",
        "X496100358",
        "X496100359",
        "X496100360",
        "X496100361",
        "X496100362",
        "X496100363",
        "X496100364",
        "X496100365",
        "X496100366",
        "X496100367",
        "X496100368",
        "X496100369",
        "X496100370",
        "X496100371",
        "X496100372",
        "X496100373",
        "X496100374",
        "X496100375",
        "X496100376",
        "X496100377",
        "X496100378",
        "X496100379",
        "X496100380",
        "X496100381",
        "X496100382",
        "X496100383",
        "X496100384",
        "X496100385",
        "X496100386",
        "X496100387",
        "X496100388",
        "X496100389",
        "X496100390",
        "X496100391",
        "X496100392",
        "X496100393",
        "X496100394",
        "X496100395",
        "X496100396",
        "X496100397",
        "X496100399",
        "X496100400",
        "X496100401",
        "X496100402",
        "X496100403",
        "X496100404",
        "X496100405",
        "X496100406",
        "X496100407",
        "X496100408",
        "X496100409",
        "X496100410",
        "X496100411",
        "X496100412",
        "X496100413",
        "X496100414",
        "X496100415",
        "X496100416",
        "X496100417",
        "X496100418",
        "X496100419",
        "X496100420",
        "X496100421",
        "X496100422",
        "X496100423",
        "X496100424",
        "X496100425",
        "X496100426",
        "X496100427",
        "X496100428",
        "X496100429",
        "X496100430",
        "X496100431",
        "X496100432",
        "X496100433",
        "X496100434",
        "X496100435",
        "X496100436",
        "X496100438",
        "X496100439",
        "X496100440",
        "X496100441",
        "X496100442",
        "X496100443",
        "X496100444",
        "X496100445",
        "X496100446",
        "X496100447",
        "X496100448",
        "X496100449",
        "X496100450",
        "X496100451",
        "X496100452",
        "X496100453",
        "X496100454",
        "X496100455",
        "X496100456",
        "X496100457",
        "X496100458",
        "X496100459",
        "X496100460",
        "X496100461",
        "X496100462",
        "X496100463",
        "X496100464",
        "X496100465",
        "X496100466",
        "X496100467",
        "X496100468",
        "X496100469",
        "X496100470",
        "X496100471",
        "X496100472",
        "X496100473",
        "X496100474",
        "X496100475",
        "X496100476",
        "X496100477",
        "X496100478",
        "X496100479",
        "X496100480",
        "X496100481",
        "X496100482",
        "X496100483",
        "X496100484",
        "X496100485",
        "X496100486",
        "X496100487",
        "X496100488",
        "X496100489",
        "X496100490",
        "X496100491",
        "X496100492",
        "X496100493",
        "X496100494",
        "X496100495",
        "X496100496",
        "X496100497",
        "X496100498",
        "X496100499",
        "X496100500",
        "X496100501",
        "X496100502",
        "X496100503",
        "X496100504",
        "X496100505",
        "X496100506",
        "X496100507",
        "X496100508",
        "X496100509",
        "X496100510",
        "X496100511",
        "X496100512",
        "X496100513",
        "X496100514",
        "X496100515",
        "X496100516",
        "X496100517",
        "X496100518",
        "X496100519",
        "X496100520",
        "X496100521",
        "X496100522",
        "X496100523",
        "X496100524",
        "X496100525",
        "X496100526",
        "X496100527",
        "X496100528",
        "X496100529",
        "X496100530",
        "X496100531",
        "X496100532",
        "X496100533",
        "X496100534",
        "X496100535",
        "X496100536",
        "X496100537",
        "X496100538",
        "X496100539",
        "X496100540",
        "X496100541",
        "X496100542",
        "X496100543",
        "X496100544",
        "X496100545",
        "X496100546",
        "X496100547",
        "X496100548",
        "X496100549",
        "X496100550",
        "X496100551",
        "X496100552",
        "X496100553",
        "X496100554",
        "X496100555",
        "X496100556",
        "X496100557",
        "X496100558",
        "X496100559",
        "X496100560",
        "X496100561",
        "X496100562",
        "X496100563",
        "X496100564",
        "X496100565",
        "X496100566",
        "X496100567",
        "X496100569",
        "X496100570",
        "X496100571",
        "X496100572",
        "X496100573",
        "X496100574",
        "X496100575",
        "X496100576",
        "X496100577",
        "X496100578",
        "X496100579",
        "X496100580",
        "X496100581",
        "X496100582",
        "X496100583",
        "X496100584",
        "X496100585",
        "X496100586",
        "X496100587",
        "X496100588",
        "X496100589",
        "X496100590",
        "X496100591",
        "X496100592",
        "X496100593",
        "X496100594",
        "X496100595",
        "X496100596",
        "X496100597",
        "X496100598",
        "X496100599",
        "X496100600",
        "X496100601",
        "X496100602",
        "X496100603",
        "X496100604",
        "X496100605",
        "X496100606",
        "X496100607",
        "X496100608",
        "X496100609",
        "X496100610",
        "X496100611",
        "X496100612",
        "X496100613",
        "X496100614",
        "X496100615",
        "X496100616",
        "X496100617",
        "X496100618",
        "X496100619",
        "X496100620",
        "X496100621",
        "X496100622",
        "X496100623",
        "X496100624",
        "X496100625",
        "X496100626",
        "X496100627",
        "X496100628",
        "X496100629",
        "X496100630",
        "X496100631",
        "X496100632",
        "X496100633",
        "X496100634",
        "X496100635",
        "X496100636",
        "X496100637",
        "X496100638",
        "X496100639",
        "X496100640",
        "X496100641",
        "X496100642",
        "X496100643",
        "X496100644",
        "X496100645",
        "X496100646",
        "X496100647",
        "X496100648",
        "X496100650",
        "X496100651",
        "X496100652",
        "X496100653",
        "X496100654",
        "X496100656",
        "X496100657",
        "X496100658",
        "X496100659",
        "X496100660",
        "X496100661",
        "X496100663",
        "X496100664",
        "X496100665",
        "X496100666",
        "X496100667",
        "X496100669",
        "X496100670",
        "X496100671",
        "X496100672"
      ],
      "rows": 395,
      "table": true,
      "tojson": true
    },
    {
      "name": "aba_pheno_data",
      "title": "Phenotype data from brain samples in the Allen Brain Atlas Aging, Dementia, and TBI study.",
      "object": "aba_pheno_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "structure_acronym.x",
        "ihc_iba1_ffpe",
        "ihc_gfap_ffpe",
        "id"
      ],
      "rows": 377,
      "table": true,
      "tojson": true
    },
    {
      "name": "kelley_df_brain",
      "title": "Marker genes estimated from",
      "object": "kelley_df_brain",
      "class": [
        "data.frame"
      ],
      "fields": [
        "markers",
        "cell"
      ],
      "rows": 84000,
      "table": true,
      "tojson": true
    },
    {
      "name": "markers_df_brain",
      "title": "Marker genes estimated from a meta-analysis of brain cell gene expression data from both humans and mice.",
      "object": "markers_df_brain",
      "class": [
        "data.frame"
      ],
      "fields": [
        "markers",
        "cell"
      ],
      "rows": 6000,
      "table": true,
      "tojson": true
    },
    {
      "name": "markers_df_human_brain",
      "title": "Marker genes estimated from a meta-analysis of brain cell gene expression data from humans only.",
      "object": "markers_df_human_brain",
      "class": [
        "data.frame"
      ],
      "fields": [
        "markers",
        "cell"
      ],
      "rows": 5500,
      "table": true,
      "tojson": true
    },
    {
      "name": "markers_df_mouse_brain",
      "title": "Marker genes estimated from a meta-analysis of brain cell gene expression data from mice only.",
      "object": "markers_df_mouse_brain",
      "class": [
        "data.frame"
      ],
      "fields": [
        "markers",
        "cell"
      ],
      "rows": 5430,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "aba_marker_expression",
      "title": "Normalized FPKM expression data from a subset of the Allen Brain Atlas Aging, Dementia, and TBI study.",
      "topics": [
        "aba_marker_expression"
      ]
    },
    {
      "page": "aba_pheno_data",
      "title": "Phenotype data from brain samples in the Allen Brain Atlas Aging, Dementia, and TBI study.",
      "topics": [
        "aba_pheno_data"
      ]
    },
    {
      "page": "adjustBrainCells",
      "title": "Estimate and adjust for brain cell type proportions in bulk expression data.",
      "topics": [
        "adjustBrainCells"
      ]
    },
    {
      "page": "adjustCells",
      "title": "Adjust for estimated cell type proportions in bulk gene expression data.",
      "topics": [
        "adjustCells"
      ]
    },
    {
      "page": "brainCells",
      "title": "Estimate brain cell type proportions in bulk expression data with marker genes.",
      "topics": [
        "brainCells"
      ]
    },
    {
      "page": "BRETIGEA",
      "title": "BRETIGEA: BRain cEll Type specIfic Gene Expression Analysis",
      "topics": [
        "BRETIGEA-package",
        "BRETIGEA"
      ]
    },
    {
      "page": "findCells",
      "title": "Find cell type proportions from bulk gene expression data using marker genes.",
      "topics": [
        "findCells"
      ]
    },
    {
      "page": "kelley_df_brain",
      "title": "Marker genes estimated from",
      "topics": [
        "kelley_df_brain"
      ]
    },
    {
      "page": "markers_df_brain",
      "title": "Marker genes estimated from a meta-analysis of brain cell gene expression data from both humans and mice.",
      "topics": [
        "markers_df_brain"
      ]
    },
    {
      "page": "markers_df_human_brain",
      "title": "Marker genes estimated from a meta-analysis of brain cell gene expression data from humans only.",
      "topics": [
        "markers_df_human_brain"
      ]
    },
    {
      "page": "markers_df_mouse_brain",
      "title": "Marker genes estimated from a meta-analysis of brain cell gene expression data from mice only.",
      "topics": [
        "markers_df_mouse_brain"
      ]
    }
  ],
  "_readme": "https://github.com/andymckenzie/bretigea/raw/HEAD/README.md",
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "BRETIGEA_basic.Rmd",
      "filename": "BRETIGEA_basic.html",
      "title": "Brain cell type proportion analysis using BRETIGEA",
      "author": "Andrew McKenzie, Minghui Wang, Bin Zhang",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Background for BRETIGEA",
        "Introduction to BRETIGEA",
        "Data loading and input format",
        "Relative cell type proportion estimation",
        "Selecting the nMarker parameter",
        "Using alternative cell type marker genes from Kelley et al.",
        "Using your own cell type marker genes",
        "Adjusting bulk gene expression data for estimated cell type proportions",
        "Help and other resources"
      ],
      "created": "2018-09-10 01:48:51",
      "modified": "2023-12-27 21:25:10",
      "commits": 3
    }
  ],
  "_score": 6.417969642214738,
  "_indexed": true,
  "_nocasepkg": "bretigea",
  "_universes": [
    "andymckenzie"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.4",
      "date": "2026-05-11T07:13:21.000Z",
      "distro": "noble",
      "commit": "b93da3fd0e7d76ccc4b58037024d17dfd3e1cfa7",
      "fileid": "33648167ccc786f7f25be57ba44bb033c2d25d5d4ff16a478c8b7e763b90512d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/andymckenzie/actions/runs/25655533729"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.4",
      "date": "2026-05-11T07:12:51.000Z",
      "distro": "noble",
      "commit": "b93da3fd0e7d76ccc4b58037024d17dfd3e1cfa7",
      "fileid": "ea077ac9fb1ea846b2e91bc2343c3348a39f0b7d00c7bc04f653b1b160c8c341",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/andymckenzie/actions/runs/25655533729"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.4",
      "date": "2026-05-11T07:12:25.000Z",
      "commit": "b93da3fd0e7d76ccc4b58037024d17dfd3e1cfa7",
      "fileid": "e087f49b600c6f11d0847246929b5f3f62054b130560e1a1cbdbfe8f66ed1002",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/andymckenzie/actions/runs/25655533729"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.4",
      "date": "2026-05-11T07:12:43.000Z",
      "commit": "b93da3fd0e7d76ccc4b58037024d17dfd3e1cfa7",
      "fileid": "0cc73f7a5a02b02b6a42e74ec76727b680d72f8cab24113b035126b84992d127",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/andymckenzie/actions/runs/25655533729"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-05-11T07:12:21.000Z",
      "commit": "b93da3fd0e7d76ccc4b58037024d17dfd3e1cfa7",
      "fileid": "c27bd0c11d94a08da8b39f3495c666b2c22cd5a9a4c82032f82a6d4be8ec6473",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/andymckenzie/actions/runs/25655533729"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-05-11T07:12:24.000Z",
      "commit": "b93da3fd0e7d76ccc4b58037024d17dfd3e1cfa7",
      "fileid": "24737f6d6951ca1fbdfc8b32554bcced5bb8e663715a645ced04ab6f793d946f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/andymckenzie/actions/runs/25655533729"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-05-11T07:13:16.000Z",
      "commit": "b93da3fd0e7d76ccc4b58037024d17dfd3e1cfa7",
      "fileid": "d02ca00f3d1223b0b889f7f3ca4220716e2520c79edd1fbaf83fd6775af0fa54",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/andymckenzie/actions/runs/25655533729"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.4",
      "date": "2026-05-22T11:49:38.000Z",
      "commit": "b93da3fd0e7d76ccc4b58037024d17dfd3e1cfa7",
      "fileid": "00e9db3aed3e8c8eb3274b63f4b40b825e14ddbe924faafe17a0bfdac577aaa5",
      "status": "success",
      "buildurl": "https://github.com/r-universe/andymckenzie/actions/runs/25655533729"
    }
  ]
}