{
  "_id": "6acde7d3a14063b82c3acb95",
  "Package": "HIREewas",
  "Type": "Package",
  "Title": "Detection of cell-type-specific risk-CpG sites in epigenome-wide\nassociation studies",
  "Version": "1.31.0",
  "Date": "2018-06-11",
  "Author": "Xiangyu Luo <xyluo1991@gmail.com>, Can Yang <macyang@ust.hk>,\nYingying Wei <yweicuhk@gmail.com>",
  "Maintainer": "Xiangyu Luo <xyluo1991@gmail.com>",
  "Description": "In epigenome-wide association studies, the measured\nsignals for each sample are a mixture of methylation profiles\nfrom different cell types. The current approaches to the\nassociation detection only claim whether a\ncytosine-phosphate-guanine (CpG) site is associated with the\nphenotype or not, but they cannot determine the cell type in\nwhich the risk-CpG site is affected by the phenotype. We\npropose a solid statistical method, HIgh REsolution (HIRE),\nwhich not only substantially improves the power of association\ndetection at the aggregated level as compared to the existing\nmethods but also enables the detection of risk-CpG sites for\nindividual cell types. The \"HIREewas\" R package is to implement\nHIRE model in R.",
  "VignetteBuilder": "knitr",
  "biocViews": "DNAMethylation, DifferentialMethylation, FeatureExtraction",
  "LazyLoad": "yes",
  "License": "GPL (>= 2)",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:54 UTC",
  "RemoteUrl": "https://github.com/bioc/HIREewas",
  "RemoteRef": "HEAD",
  "RemoteSha": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-12 13:29:17 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "HIREewas_1.31.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/ae468d41ab3d7433de23edbe2c36ebee6b1d4a80da603c20188ea881c8cef0bd",
  "_filesize": 378696,
  "_sha256": "ae468d41ab3d7433de23edbe2c36ebee6b1d4a80da603c20188ea881c8cef0bd",
  "_expires": "2027-01-20T13:35:45.000Z",
  "_created": "2026-10-12T13:29:17.000Z",
  "_published": "2026-10-13T08:12:03.353Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 8
  },
  "_upstream": "https://github.com/bioc/HIREewas",
  "_commit": {
    "id": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
    "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": 1777380534
  },
  "_maintainer": {
    "name": "Xiangyu Luo",
    "email": "xyluo1991@gmail.com",
    "login": "xiangyuluo",
    "description": "\n    Associate Professor (with tenure), Institute of Statistics and Big Data,  Renmin University of China\n",
    "uuid": 25922838
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 115195146355,
      "time": 118,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11797253561"
    },
    {
      "job": 115195148179,
      "time": 117,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11750342496"
    },
    {
      "job": 115195148155,
      "time": 181,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11750696843"
    },
    {
      "job": 115195148854,
      "time": 125,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11750077815"
    },
    {
      "job": 115195148636,
      "time": 353,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11750637439"
    },
    {
      "job": 115195148959,
      "time": 123,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11749988099"
    },
    {
      "job": 115195148027,
      "time": 312,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11750857173"
    },
    {
      "job": 115195147839,
      "time": 114,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11750027862"
    },
    {
      "job": 115195148035,
      "time": 219,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11750327833"
    },
    {
      "job": 115195147424,
      "time": 247,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11749602980"
    },
    {
      "job": 115195148462,
      "time": 82,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11750412084"
    },
    {
      "job": 115195146462,
      "time": 207,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11797670950"
    },
    {
      "job": 115195147860,
      "time": 195,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11749943235"
    },
    {
      "job": 115195148056,
      "time": 126,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11750641772"
    },
    {
      "job": 115195148859,
      "time": 348,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11750333063"
    },
    {
      "job": 115195148638,
      "time": 99,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11749558398"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "quadprog",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "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": "1.31.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "dnamethylation",
    "differentialmethylation",
    "featureextraction"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 390,
    "source": "https://www.bioconductor.org/packages/stats/bioc/HIREewas"
  },
  "_searchresults": 1,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/HIREewas.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "HIRE",
    "riskCpGpattern"
  ],
  "_help": [
    {
      "page": "HIREewas-package",
      "title": "Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies",
      "topics": [
        "HIREewas-package",
        "HIREewas"
      ]
    },
    {
      "page": "HIRE",
      "title": "Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies",
      "topics": [
        "HIRE"
      ]
    },
    {
      "page": "riskCpGpattern",
      "title": "Plot the detected association pattern with one phenotype using heatmap",
      "topics": [
        "riskCpGpattern"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/HIREewas/raw/HEAD/README.md",
  "_rundeps": [
    "bitops",
    "caTools",
    "gplots",
    "gtools",
    "KernSmooth",
    "quadprog"
  ],
  "_vignettes": [
    {
      "source": "HIREewas.Rnw",
      "filename": "HIREewas.pdf",
      "title": "HIREewas",
      "engine": "knitr::knitr",
      "headings": [
        "1 Introduction",
        "2 Data Preparation",
        "3 Model Application",
        "4 Visualization"
      ],
      "created": "2018-09-12 07:44:38",
      "modified": "2018-12-01 04:51:38",
      "commits": 6
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "hireewas",
  "_universes": [
    "bioc",
    "xiangyuluo"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-10-12T13:31:03.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/f9ba8b057e8e3315ac05c20c45bf79fa9ff9df247f8259b41f9562dbebf43815",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-10-12T13:31:54.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/d38acd8fab156b9a46919632e9560669bad308091a15680a51314e8d156739eb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-10-12T13:31:05.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/fa561781cd6b4a8e1ea0eb72ec36d8ec4844c7e0d5a27517c2b23f4760cb5aa7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-10-12T13:34:51.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/0e6741de82b2930e188ce392a66982131a2b030e53dd4ba865781aa418c1a0b4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-10-12T13:31:03.000Z",
      "arch": "aarch64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/474a4604da3fe2d1d92bfeaa31e986a9c7879f23d7aacfabf24669fe07f7682f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-10-12T13:33:30.000Z",
      "arch": "x86_64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/bd67ba63effe749f86d3e52476a71fe23491f501d6eb8510da5dcb7187f28492",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-10-12T13:31:00.000Z",
      "arch": "aarch64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/5bd135ef57996bd8ee2acb90eca89bdb8a38c4e0ea88ed64e83c4eb7bf95dab3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-10-12T13:32:03.000Z",
      "arch": "x86_64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/d8660253bb161e03c2dc07c56494946aa7a72db32c1e23bf5c55756c460626c3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.0",
      "date": "2026-10-12T13:30:58.000Z",
      "arch": "emscripten",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/c7ecb7c2dc3149055a1747b66cfcb49c8bb9864832618df02a8feaac22f75dff",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-10-13T08:10:48.000Z",
      "arch": "aarch64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/3429e175ecd89e71b3c7b3f6497bba52a8cc15a67f77f5c88b0b6902963302a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-10-12T13:31:13.000Z",
      "arch": "x86_64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/f7b643a8655e5fe0aa4fa67b8112c6a002141b8ae07ef2fe253b7b6310face8c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-10-12T13:30:30.000Z",
      "arch": "x86_64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/bccf8eeb5d4bb1f51af2da0343ace5fb0410ee6b3b96491cb895bed90b5c33d1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-10-12T13:34:26.000Z",
      "arch": "aarch64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/80a0015d9c26ce083f62ecc8da2b648fa1ad31f52f88d2362e4b43bb49a3744e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-10-12T13:30:24.000Z",
      "arch": "x86_64",
      "commit": "7edc56bd5c44cfd118989ad46daf8fe993f4aae8",
      "fileid": "https://r2.ropensci.org/b2364eecd6720d529da28e1d46c7b4a2e564451b436e9084f28cd194610d2269",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38255538027"
    }
  ]
}