{
  "_id": "6aca5b6dfe5cc25786e87c1e",
  "Package": "HIREewas",
  "Type": "Package",
  "Title": "Detection of cell-type-specific risk-CpG sites in epigenome-wide\nassociation studies",
  "Version": "1.30.0",
  "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": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:48:54 UTC",
  "RemoteUrl": "https://github.com/bioc/HIREewas",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-10 14:33:52 UTC",
    "User": "root"
  },
  "_user": "bioc-release",
  "_type": "src",
  "_file": "HIREewas_1.30.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/beef457355049f6a34c0efcf4dc3c48c3da5a77e0b409c7939c965bdd60ea221",
  "_filesize": 378884,
  "_sha256": "beef457355049f6a34c0efcf4dc3c48c3da5a77e0b409c7939c965bdd60ea221",
  "_expires": "2027-01-18T15:36:11.000Z",
  "_created": "2026-10-10T14:33:52.000Z",
  "_published": "2026-10-10T15:36:13.421Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 9
  },
  "_upstream": "https://github.com/bioc/HIREewas",
  "_commit": {
    "id": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
    "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": 1777380534
  },
  "_maintainer": {
    "name": "Xiangyu Luo",
    "email": "xyluo1991@gmail.com",
    "login": "xiangyuluo",
    "uuid": 25922838
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114236536612,
      "time": 131,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11672184138"
    },
    {
      "job": 114236536618,
      "time": 116,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11672179112"
    },
    {
      "job": 114236536670,
      "time": 207,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11672204087"
    },
    {
      "job": 114236536645,
      "time": 117,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11673285790"
    },
    {
      "job": 114236536748,
      "time": 174,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11672698297"
    },
    {
      "job": 114236536643,
      "time": 96,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11674440500"
    },
    {
      "job": 114236536731,
      "time": 519,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11673313531"
    },
    {
      "job": 114236536759,
      "time": 102,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11674680603"
    },
    {
      "job": 114236536730,
      "time": 276,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11673971526"
    },
    {
      "job": 114235675951,
      "time": 252,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11673320490"
    },
    {
      "job": 114236536636,
      "time": 83,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11673001109"
    },
    {
      "job": 114236536728,
      "time": 222,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11672658344"
    },
    {
      "job": 114236536755,
      "time": 106,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11672253807"
    },
    {
      "job": 114236536673,
      "time": 114,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11672603288"
    },
    {
      "job": 114236536727,
      "time": 239,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11673315841"
    },
    {
      "job": 114236536685,
      "time": 71,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11672643119"
    }
  ],
  "_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": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_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/RELEASE_3_23/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": false,
  "_nocasepkg": "hireewas",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/HIREewas",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.30.0",
      "date": "2026-10-10T14:35:40.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/a77d138a0ff3b041c882c7cabe161f59310664e589f7f8b97af0ae143d1f3796",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.30.0",
      "date": "2026-10-10T14:37:06.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/fa2705551d7c649995ebe62070cbcdf78e471c8e706e3aa975f28640d829fc09",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.30.0",
      "date": "2026-10-10T14:35:42.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/df0855d10d4c0cbf662184a213e5280d85ef33885518a9182902dbd5a36d3bd1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.30.0",
      "date": "2026-10-10T14:36:28.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/9cc91040fa109041dea4000bb159ce4136403616b42af22bfa375a8948e2e2de",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.30.0",
      "date": "2026-10-10T15:33:00.000Z",
      "arch": "aarch64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/7d8438851eff8a4048c5edcd6ccd4b2984faeddc64968fafa24c78a413adc6f8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.30.0",
      "date": "2026-10-10T15:08:46.000Z",
      "arch": "x86_64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/b48c1f4cb17bee13391ec2410d186e6a46eb61f8807c416632b5d7e4182df2de",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.30.0",
      "date": "2026-10-10T15:35:22.000Z",
      "arch": "aarch64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/78b09c08d1e249eac6574c44968bd5f6e670319d52978d3d90ec01e42ba2c57a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.30.0",
      "date": "2026-10-10T15:04:28.000Z",
      "arch": "x86_64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/a9312c2a9c94923db24fd7e7de0031d4f998b8e6d7ce318d712abbe84d2f0c86",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.30.0",
      "date": "2026-10-10T14:35:38.000Z",
      "arch": "emscripten",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/40554450c7563384403b1acf9c975820ed9664d3236c3f61ac31227d34b45587",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-10-10T14:37:00.000Z",
      "arch": "aarch64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/6114d5728db15cd0e2670a9534877ddbe19fa4d1ac5ea6643d1c4df867a6104e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-10-10T14:34:55.000Z",
      "arch": "x86_64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/330db2e14c0a4b72725fdeaa4226f8b81df8a1492416e448df4fdfc5c9c576f2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-10-10T14:35:04.000Z",
      "arch": "x86_64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/e265e6cead9ccb7fe11478d032da7ff69ee8cb93ab1c0045e8e6c6ffd9489af2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-10-10T14:37:18.000Z",
      "arch": "aarch64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/00473d8bc41b04850c5056046179966b907ff75ca3652fe8701963a65d59b1a9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.30.0",
      "date": "2026-10-10T14:34:50.000Z",
      "arch": "x86_64",
      "commit": "a5e69b029bcf240dba4e6ab8498329ee048af69b",
      "fileid": "https://r2.ropensci.org/34ac7dd2bfcf2941ec420f36d2d5f605571353601afb8e98646f1e50770d8ecc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38059820265"
    }
  ]
}