{
  "_id": "6a5c60039baadeef8ab4f35b",
  "Package": "MiChip",
  "Version": "1.67.0",
  "Date": "2009-09-10",
  "Title": "MiChip Parsing and Summarizing Functions",
  "Author": "Jonathon Blake <blake@embl.de>",
  "Maintainer": "Jonathon Blake <blake@embl.de>",
  "Description": "This package takes the MiChip miRNA microarray .grp\nscanner output files and parses these out, providing summary\nand plotting functions to analyse MiChip hybridizations. A set\nof hybridizations is packaged into an ExpressionSet allowing it\nto be used by other BioConductor packages.",
  "License": "GPL (>= 2)",
  "biocViews": "Microarray, Preprocessing",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:11 UTC",
  "RemoteUrl": "https://github.com/bioc/MiChip",
  "RemoteRef": "HEAD",
  "RemoteSha": "7fa093864888a11045dec1f78ec6f07050f1269b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-19 05:22:51 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "MiChip_1.67.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b3bb87ed2d1d9a92bf5930d03aabff0bd2f6fdedfa4592a6cd43402ddd440e86",
  "_filesize": 665092,
  "_sha256": "b3bb87ed2d1d9a92bf5930d03aabff0bd2f6fdedfa4592a6cd43402ddd440e86",
  "_expires": "2026-10-27T05:26:25.000Z",
  "_created": "2026-07-19T05:22:51.000Z",
  "_published": "2026-07-19T05:26:27.119Z",
  "_bioccheck": {
    "error": 2,
    "warning": 4,
    "note": 15
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29674675481",
  "_status": "success",
  "_upstream": "https://github.com/bioc/MiChip",
  "_commit": {
    "id": "7fa093864888a11045dec1f78ec6f07050f1269b",
    "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": 1777379651
  },
  "_maintainer": {
    "name": "Jonathon Blake",
    "email": "blake@embl.de",
    "login": "jonathonblake",
    "description": "",
    "uuid": 5990187
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 88159998803,
      "time": 146,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8438492845"
    },
    {
      "job": 88159998822,
      "time": 176,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8438497553"
    },
    {
      "job": 88159998845,
      "time": 172,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8438496753"
    },
    {
      "job": 88159998811,
      "time": 94,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8438484331"
    },
    {
      "job": 88159998815,
      "time": 85,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8438482873"
    },
    {
      "job": 88159765361,
      "time": 181,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8438469318"
    },
    {
      "job": 88159998808,
      "time": 89,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8438483550"
    },
    {
      "job": 88159998832,
      "time": 69,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8438480343"
    },
    {
      "job": 88159998834,
      "time": 88,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8438483663"
    },
    {
      "job": 88159998825,
      "time": 68,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8438480358"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.3.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.67.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.66.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "preprocessing"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 449,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 438,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MiChip"
  },
  "_searchresults": 3,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MiChip.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "boxplotData",
    "boxplotDataNoFile",
    "correctForFlags",
    "myForgivingMedian",
    "normalizePerChipMedian",
    "outputAnnotatedDataMatrix",
    "parseRawData",
    "plotIntensitiesScatter",
    "removeUnwantedRows",
    "returnAnnotatedDataMatrix",
    "setIntensityCutoff",
    "standardRemoveRows",
    "summarizeIntensitiesAsMedian",
    "workedExampleMedianNormalize",
    "workedExampleNotNormalizedData"
  ],
  "_help": [
    {
      "page": "boxplotData",
      "title": "Create Boxplot of data",
      "topics": [
        "boxplotData"
      ]
    },
    {
      "page": "boxplotDataNoFile",
      "title": "Create Boxplot of data",
      "topics": [
        "boxplotDataNoFile"
      ]
    },
    {
      "page": "correctForFlags",
      "title": "Corrects for spots flagged as not present",
      "topics": [
        "correctForFlags"
      ]
    },
    {
      "page": "MiChip",
      "title": "Introduction to the MiChip Package",
      "topics": [
        "Introduction",
        "MiChip"
      ]
    },
    {
      "page": "myForgivingMedian",
      "title": "Produce Median from Probe Intensity values",
      "topics": [
        "myForgivingMedian"
      ]
    },
    {
      "page": "naOmitMedian",
      "title": "Calculates the median of an array excluding NAs",
      "topics": [
        "naOmitMedian"
      ]
    },
    {
      "page": "normalizePerChipMedian",
      "title": "Normalize to median intensity",
      "topics": [
        "normalizePerChipMedian"
      ]
    },
    {
      "page": "outputAnnotatedDataMatrix",
      "title": "Outputs a tab delimited file from an ExpressionSet",
      "topics": [
        "outputAnnotatedDataMatrix"
      ]
    },
    {
      "page": "panelCor",
      "title": "Add Pearson Correlation value to plots",
      "topics": [
        "panelCor"
      ]
    },
    {
      "page": "parseRawData",
      "title": "Parse raw data files to create an ExpressionSet",
      "topics": [
        "parseRawData"
      ]
    },
    {
      "page": "plotIntensitiesScatter",
      "title": "Plot pairwise intensity scatter",
      "topics": [
        "plotIntensitiesScatter"
      ]
    },
    {
      "page": "removeUnwantedRows",
      "title": "Removes unwanted rows from data matrix",
      "topics": [
        "removeUnwantedRows"
      ]
    },
    {
      "page": "returnAnnotatedDataMatrix",
      "title": "returns and annotated data matrix from an ExpressionSet",
      "topics": [
        "returnAnnotatedDataMatrix"
      ]
    },
    {
      "page": "setIntensityCutoff",
      "title": "Sets a cutoff for the lowest intensity value",
      "topics": [
        "setIntensityCutoff"
      ]
    },
    {
      "page": "standardRemoveRows",
      "title": "Removes a standard list of features for MiChip processing",
      "topics": [
        "standardRemoveRows"
      ]
    },
    {
      "page": "summarizeIntensitiesAsMedian",
      "title": "Summarizes the probe intensity as median of replicates spotted",
      "topics": [
        "summarizeIntensitiesAsMedian"
      ]
    },
    {
      "page": "workedExampleMedianNormalize",
      "title": "Worked Example of MiChip Processing",
      "topics": [
        "workedExampleMedianNormalize"
      ]
    },
    {
      "page": "workedExampleNotNormalizedData",
      "title": "Worked Example of MiChip Processing",
      "topics": [
        "workedExampleNotNormalizedData"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "generics"
  ],
  "_vignettes": [
    {
      "source": "MiChip.Rnw",
      "filename": "MiChip.pdf",
      "title": "MiChip miRNA Microarray Processing",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Reading the Hybridization Files",
        "Removing Unwanted Rows and Correcting for Flags",
        "Summarizing Intensities",
        "Plotting Functions",
        "Normalization",
        "Writing Output Files",
        "Combination of processes"
      ],
      "created": "2013-11-01 20:09:52",
      "modified": "2013-11-01 20:09:52",
      "commits": 1
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "michip",
  "_universes": [
    "bioc",
    "jonathonblake"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.67.0",
      "date": "2026-07-19T05:25:50.000Z",
      "distro": "resolute",
      "commit": "7fa093864888a11045dec1f78ec6f07050f1269b",
      "fileid": "https://r2.ropensci.org/8bb06cc0a105524bf77b766360364f9b23e652a3475c2c053f10c9b6bb77f4c9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29674675481"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.67.0",
      "date": "2026-07-19T05:25:45.000Z",
      "distro": "resolute",
      "commit": "7fa093864888a11045dec1f78ec6f07050f1269b",
      "fileid": "https://r2.ropensci.org/f268327602c30bc31507dbe5e9006ff1382127810f8047d74d38fa37aa95b7c6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29674675481"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.67.0",
      "date": "2026-07-19T05:24:33.000Z",
      "commit": "7fa093864888a11045dec1f78ec6f07050f1269b",
      "fileid": "https://r2.ropensci.org/ae3912e3b0f10ebafb85c5fae12d1da105bb6fd18cc1d81a8b570ddb67041c67",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29674675481"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.67.0",
      "date": "2026-07-19T05:24:23.000Z",
      "commit": "7fa093864888a11045dec1f78ec6f07050f1269b",
      "fileid": "https://r2.ropensci.org/f9fec97bc6e32b11d8231ff77bbc76610e59ac833de9d3451d382835d2987a7d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29674675481"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.67.0",
      "date": "2026-07-19T05:24:40.000Z",
      "commit": "7fa093864888a11045dec1f78ec6f07050f1269b",
      "fileid": "https://r2.ropensci.org/202556fd13cad03837aafc2c629df336bfddcdf8922dfdfe2c4d90a0e6d6a426",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29674675481"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.67.0",
      "date": "2026-07-19T05:23:58.000Z",
      "commit": "7fa093864888a11045dec1f78ec6f07050f1269b",
      "fileid": "https://r2.ropensci.org/dcfc4c41b405dafe34ff738d8c778da3a6b3bdc0ec1110e3d8c106188a3df109",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29674675481"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.67.0",
      "date": "2026-07-19T05:24:20.000Z",
      "commit": "7fa093864888a11045dec1f78ec6f07050f1269b",
      "fileid": "https://r2.ropensci.org/584c969ab5709a2ef316e406bfdbf52342cdab2131209a9e31cb1b4a01ed40c5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29674675481"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.67.0",
      "date": "2026-07-19T05:23:58.000Z",
      "commit": "7fa093864888a11045dec1f78ec6f07050f1269b",
      "fileid": "https://r2.ropensci.org/2dfa67985d8b95ecb7980ab53006f4fa1eee4252a72fa8f36d13d06f42bb636a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29674675481"
    }
  ]
}