{
  "_id": "6aca1de1fe5cc25786e84d8a",
  "Package": "HarmanData",
  "Type": "Package",
  "Title": "Data for the Harman package",
  "Version": "1.40.0",
  "Date": "2022-02-18",
  "Authors@R": "c(person(given = \"Yalchin\",\nfamily=\"Oytam\",\nemail = \"Yalchin.Oytam@health.nsw.gov.au\",\nrole = \"aut\"),\nperson(given=\"Josh\",\nfamily=\"Bowden\",\nrole = \"aut\"),\nperson(given=\"Jason\",\nfamily=\"Ross\",\nemail = \"jason.ross@csiro.au\",\nrole = c(\"aut\", \"cre\")))",
  "Description": "Datasets of accompany Harman, a PCA and constrained\noptimisation based technique. Contains three example datasets:\nIMR90, Human lung fibroblast cells exposed to nitric oxide;\nNPM, an experiment to test skin penetration of metal oxide\nnanoparticles following topical application of sunscreens in\nnon-pregnant mice; OLF; an experiment to gauge the response of\nhuman olfactory neurosphere-derived (hONS) cells to ZnO\nnanoparticles. Since version 1.24, this package also contains\nthe Infinium5 dataset, a set of batch correction adjustments\nacross 5 Illumina Infinium Methylation BeadChip datasets. This\nfile does not contain methylation data, but summary statistics\nof 5 datasets after correction. There is also an\nEpiSCOPE_sample file as exampling for the new methylation\nclustering functionality in Harman.",
  "NeedsCompilation": "no",
  "License": "GPL-3",
  "LazyData": "true",
  "LazyDataCompression": "gzip",
  "VignetteBuilder": "knitr",
  "biocViews": "ExpressionData, MicroarrayData, ExperimentData,\nHomo_sapiens_Data, Mus_musculus_Data",
  "URL": "http://www.bioinformatics.csiro.au/harman/",
  "RoxygenNote": "7.1.2",
  "Encoding": "UTF-8",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:29:45 UTC",
  "RemoteUrl": "https://github.com/bioc/HarmanData",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "3671f37ef590995e71f445f0cf445e959ab1b916",
  "Packaged": {
    "Date": "2026-10-10 11:09:01 UTC",
    "User": "root"
  },
  "Author": "Yalchin Oytam [aut],\nJosh Bowden [aut],\nJason Ross [aut, cre]",
  "Maintainer": "Jason Ross <jason.ross@csiro.au>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "HarmanData_1.40.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/9dc47dcb29bbf46cd90e0558618e59cf6b193e60b845af2d294bd215e2858fcd",
  "_filesize": 57188626,
  "_sha256": "9dc47dcb29bbf46cd90e0558618e59cf6b193e60b845af2d294bd215e2858fcd",
  "_expires": "2027-01-18T11:13:34.000Z",
  "_created": "2026-10-10T11:09:01.000Z",
  "_published": "2026-10-10T11:13:37.620Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047222510",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 10
  },
  "_upstream": "https://github.com/bioc/HarmanData",
  "_commit": {
    "id": "3671f37ef590995e71f445f0cf445e959ab1b916",
    "author": "lshep <lori.shepherd@roswellpark.org>",
    "committer": "lshep <lori.shepherd@roswellpark.org>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379385
  },
  "_maintainer": {
    "name": "Jason Ross",
    "email": "jason.ross@csiro.au",
    "login": "jasonr055",
    "description": "",
    "uuid": 1931007
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114199678052,
      "time": 133,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11668296713"
    },
    {
      "job": 114199678105,
      "time": 168,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11668306668"
    },
    {
      "job": 114199678070,
      "time": 196,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11668361623"
    },
    {
      "job": 114199126375,
      "time": 197,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11668241490"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "Harman",
      "version": ">= 1.23.3",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24",
      "repository": "data/experiment"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23",
      "repository": "data/experiment"
    }
  ],
  "_topics": [
    "expressiondata",
    "microarraydata",
    "experimentdata",
    "homo_sapiens_data",
    "mus_musculus_data",
    "datapkg"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_searchresults": 50,
  "_datapkg": true,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/HarmanData.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_cranurl": false,
  "_exports": [],
  "_datasets": [
    {
      "name": "episcope",
      "title": "Infinium Methylation BeadChip batch correction reference data",
      "object": "episcope",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "imr90.data",
      "title": "IMR90 data, a Human lung fibroblast cell line.",
      "object": "IMR90",
      "class": [
        "data.frame"
      ],
      "fields": [
        "X_23_1CON",
        "X_23_2CON",
        "X_23_3NO0",
        "X_23_4NO7",
        "X_26_1CON",
        "X_26_2CON",
        "X_26_3NO0",
        "X_26_4NO7",
        "CONTROLZ",
        "CONTROL7",
        "NO_ZERO",
        "NO_7_5"
      ],
      "rows": 22223,
      "table": true,
      "tojson": true
    },
    {
      "name": "imr90.info",
      "title": "IMR90 data, a Human lung fibroblast cell line.",
      "object": "IMR90",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Treatment",
        "Batch"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    },
    {
      "name": "lvr.combat",
      "title": "Infinium Methylation BeadChip batch correction reference data",
      "object": "Infinium5",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "EpiSCOPE_var_ratio_combat",
        "EPIC-Italy_var_ratio_combat",
        "BodyFatness_var_ratio_combat",
        "NOVI_var_ratio_combat",
        "URECA_var_ratio_combat"
      ],
      "rows": 899255,
      "table": true,
      "tojson": true
    },
    {
      "name": "lvr.harman",
      "title": "Infinium Methylation BeadChip batch correction reference data",
      "object": "Infinium5",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "EpiSCOPE_var_ratio_harman",
        "EPIC-Italy_var_ratio_harman",
        "BodyFatness_var_ratio_harman",
        "NOVI_var_ratio_harman",
        "URECA_var_ratio_harman"
      ],
      "rows": 899255,
      "table": true,
      "tojson": true
    },
    {
      "name": "md.combat",
      "title": "Infinium Methylation BeadChip batch correction reference data",
      "object": "Infinium5",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "EpiSCOPE_meandiffs_combat",
        "EPIC-Italy_meandiffs_combat",
        "BodyFatness_meandiffs_combat",
        "NOVI_meandiffs_combat",
        "URECA_meandiffs_combat"
      ],
      "rows": 899255,
      "table": true,
      "tojson": true
    },
    {
      "name": "md.harman",
      "title": "Infinium Methylation BeadChip batch correction reference data",
      "object": "Infinium5",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "EpiSCOPE_meandiffs_harman",
        "EPIC-Italy_meandiffs_harman",
        "BodyFatness_meandiffs_harman",
        "NOVI_meandiffs_harman",
        "URECA_meandiffs_harman"
      ],
      "rows": 899255,
      "table": true,
      "tojson": true
    },
    {
      "name": "npm.data",
      "title": "Non-pregant mice study data",
      "object": "NPM",
      "class": [
        "data.frame"
      ],
      "fields": [
        "c1",
        "c2",
        "c3",
        "c4",
        "c5",
        "c6",
        "c7",
        "c8",
        "c9",
        "c10",
        "c11",
        "c12",
        "c13",
        "c14",
        "c15",
        "c16",
        "c17",
        "c18",
        "c19",
        "c20",
        "c21",
        "c22",
        "c23",
        "c24"
      ],
      "rows": 35512,
      "table": true,
      "tojson": true
    },
    {
      "name": "npm.info",
      "title": "Non-pregant mice study data",
      "object": "NPM",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Treatment",
        "Batch"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "olf.data",
      "title": "Olfactory stem cell study data",
      "object": "OLF",
      "class": [
        "data.frame"
      ],
      "fields": [
        "c1",
        "c2",
        "c3",
        "c4",
        "c5",
        "c6",
        "c7",
        "c8",
        "c9",
        "c10",
        "c11",
        "c12",
        "c13",
        "c14",
        "c15",
        "c16",
        "c17",
        "c18",
        "c19",
        "c20",
        "c21",
        "c22",
        "c23",
        "c24",
        "c25",
        "c26",
        "c27",
        "c28"
      ],
      "rows": 33297,
      "table": true,
      "tojson": true
    },
    {
      "name": "olf.info",
      "title": "Olfactory stem cell study data",
      "object": "OLF",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Treatment",
        "Batch"
      ],
      "rows": 28,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "episcope",
      "title": "Infinium Methylation BeadChip batch correction reference data",
      "topics": [
        "episcope"
      ]
    },
    {
      "page": "IMR90",
      "title": "IMR90 data, a Human lung fibroblast cell line.",
      "topics": [
        "IMR90",
        "imr90.data",
        "imr90.info"
      ]
    },
    {
      "page": "Infinium5",
      "title": "Infinium Methylation BeadChip batch correction reference data",
      "topics": [
        "Infinium5",
        "lvr.combat",
        "lvr.harman",
        "md.combat",
        "md.harman"
      ]
    },
    {
      "page": "NPM",
      "title": "Non-pregant mice study data",
      "topics": [
        "NPM",
        "npm.data",
        "npm.info"
      ]
    },
    {
      "page": "OLF",
      "title": "Olfactory stem cell study data",
      "topics": [
        "OLF",
        "olf.data",
        "olf.info"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/HarmanData/raw/RELEASE_3_23/README.md",
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "HarmanData.Rmd",
      "filename": "HarmanData.html",
      "title": "HarmanData",
      "engine": "knitr::rmarkdown",
      "headings": [
        "title: \"HarmanData: example and reference data to use with batch correction package Harman\"author: \"Jason Ross and Yalchin Oytam\"date: \"r doc_date()\"package: \"r pkg_ver('HarmanData')\"output:BiocStyle::html_documentvignette: >%\\VignetteIndexEntry",
        "Overview",
        "Example gene expression data",
        "IMR90",
        "NPM",
        "OLF",
        "Usage",
        "Methylation reference data",
        "Infinium5",
        "episcope",
        "References"
      ],
      "created": "2016-04-14 20:32:35",
      "modified": "2022-03-15 05:31:29",
      "commits": 4
    }
  ],
  "_score": 4.698970004336019,
  "_indexed": false,
  "_nocasepkg": "harmandata",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/HarmanData",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.40.0",
      "date": "2026-10-10T11:12:00.000Z",
      "distro": "resolute",
      "commit": "3671f37ef590995e71f445f0cf445e959ab1b916",
      "fileid": "https://r2.ropensci.org/32ce0a1ab0640afe9cecd7ed33b7ef5aeb171a0a98f9a08ebaf8679540b13cee",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047222510"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.40.0",
      "date": "2026-10-10T11:12:32.000Z",
      "distro": "resolute",
      "commit": "3671f37ef590995e71f445f0cf445e959ab1b916",
      "fileid": "https://r2.ropensci.org/bbc90e7898f5d89f95ac878126dffcb01f28d11e5f6597699043ce8acb9a46e1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047222510"
    }
  ]
}