{
  "_id": "6acdf120a14063b82c3ad4f8",
  "Package": "ExiMiR",
  "Type": "Package",
  "Title": "R functions for the normalization of Exiqon miRNA array data",
  "Version": "2.54.0",
  "Date": "2012-11-06",
  "Author": "Sylvain Gubian <DL.RSupport@pmi.com>, Alain Sewer\n<DL.RSupport@pmi.com>, PMP SA",
  "Maintainer": "Sylvain Gubian <DL.RSupport@pmi.com>",
  "Description": "This package contains functions for reading raw data in\nImaGene TXT format obtained from Exiqon miRCURY LNA arrays,\nannotating them with appropriate GAL files, and normalizing\nthem using a spike-in probe-based method. Other platforms and\ndata formats are also supported.",
  "License": "GPL-2",
  "Collate": "make.gal.env.R read.exi.R createAB.R NormiR.R NormiR.methods.R",
  "LazyLoad": "yes",
  "biocViews": "Microarray, OneChannel, TwoChannel, Preprocessing,\nGeneExpression, Transcription",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:35:05 UTC",
  "RemoteUrl": "https://github.com/bioc/ExiMiR",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "e275382de8434f98136da6c0ca69eba8db61b114",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-13 08:34:30 UTC",
    "User": "root"
  },
  "_user": "bioc-release",
  "_type": "src",
  "_file": "ExiMiR_2.54.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b4028fd9f3ab11cea450186868e1cd5ba1edd51c54445ae29826bc787da589d7",
  "_filesize": 1393202,
  "_sha256": "b4028fd9f3ab11cea450186868e1cd5ba1edd51c54445ae29826bc787da589d7",
  "_expires": "2027-01-21T08:51:42.000Z",
  "_created": "2026-10-13T08:34:30.000Z",
  "_published": "2026-10-13T08:51:43.849Z",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38369713286",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 16
  },
  "_upstream": "https://github.com/bioc/ExiMiR",
  "_commit": {
    "id": "e275382de8434f98136da6c0ca69eba8db61b114",
    "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": 1777379705
  },
  "_maintainer": {
    "name": "Sylvain Gubian",
    "email": "dl.rsupport@pmi.com"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 115205053897,
      "time": 137,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11799115433"
    },
    {
      "job": 115205053832,
      "time": 292,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11799111031"
    },
    {
      "job": 115205053790,
      "time": 182,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11798823961"
    },
    {
      "job": 115205053795,
      "time": 123,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11800260532"
    },
    {
      "job": 115205053729,
      "time": 146,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11800265310"
    },
    {
      "job": 115203525827,
      "time": 238,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11798772691"
    },
    {
      "job": 115205053923,
      "time": 96,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11798653330"
    },
    {
      "job": 115205053990,
      "time": 467,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11798967383"
    },
    {
      "job": 115205053865,
      "time": 400,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11798794026"
    },
    {
      "job": 115205053803,
      "time": 330,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11799190813"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "version": ">= 2.5.5",
      "role": "Depends"
    },
    {
      "package": "affy",
      "version": ">= 1.26.1",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Depends"
    },
    {
      "package": "affyio",
      "version": ">= 1.13.3",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "version": ">= 2.5.5",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "version": ">= 1.10.0",
      "role": "Imports"
    },
    {
      "package": "mirna10cdf",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.55.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "2.54.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "microarray",
    "onechannel",
    "twochannel",
    "preprocessing",
    "geneexpression",
    "transcription"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 604,
    "source": "https://www.bioconductor.org/packages/stats/bioc/ExiMiR"
  },
  "_mentions": 3,
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/ExiMiR.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "LICENSE"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bg.correct.miR",
    "createAB",
    "make.gal.env",
    "norm.miR",
    "NormiR",
    "NormiR.bgcorrect.methods",
    "NormiR.normalize.methods",
    "NormiR.pmcorrect.methods",
    "NormiR.spikein.args",
    "NormiR.summary.methods",
    "ReadExi",
    "summarize.miR"
  ],
  "_datasets": [
    {
      "name": "galenv",
      "title": "R annotation environment for GEO series GSE20122",
      "object": "galenv",
      "file": "galenv.rda",
      "class": [
        "environment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "GSE19183",
      "title": "Affybatch object for the raw data from GEO series GSE19183",
      "object": "GSE19183",
      "file": "GSE19183.rda",
      "class": [
        "AffyBatch"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "GSE20122",
      "title": "Affybatch object for the raw data from GEO series GSE20122",
      "object": "GSE20122",
      "file": "GSE20122.rda",
      "class": [
        "AffyBatch"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ExiMiR-package",
      "title": "R functions for the normalization of Exiqon miRNA array data",
      "topics": [
        "ExiMiR"
      ]
    },
    {
      "page": "bg.correct.miR",
      "title": "ExiMiR low-level function for background correction",
      "topics": [
        "bg.correct.miR"
      ]
    },
    {
      "page": "createAB",
      "title": "ExiMiR function for creating an AffyBatch object from other object types (RGList, EListRaw, MAList or list)",
      "topics": [
        "createAB"
      ]
    },
    {
      "page": "galenv",
      "title": "R annotation environment for GEO series GSE20122",
      "topics": [
        "galenv"
      ]
    },
    {
      "page": "GSE19183",
      "title": "Affybatch object for the raw data from GEO series GSE19183",
      "topics": [
        "GSE19183"
      ]
    },
    {
      "page": "GSE20122",
      "title": "Affybatch object for the raw data from GEO series GSE20122",
      "topics": [
        "GSE20122"
      ]
    },
    {
      "page": "make.gal.env",
      "title": "GAL Environment Maker",
      "topics": [
        "make.gal.env"
      ]
    },
    {
      "page": "norm.miR",
      "title": "ExiMiR low-level function for miRNA raw data normalization.",
      "topics": [
        "norm.miR"
      ]
    },
    {
      "page": "NormiR",
      "title": "ExiMiR high-level function for miRNA raw data normalization.",
      "topics": [
        "NormiR"
      ]
    },
    {
      "page": "NormiR.methods",
      "title": "ExiMiR functions for enumerating the names of low-level normalization methods or arguments",
      "topics": [
        "NormiR.bgcorrect.methods",
        "NormiR.normalize.methods",
        "NormiR.pmcorrect.methods",
        "NormiR.spikein.args",
        "NormiR.summary.methods"
      ]
    },
    {
      "page": "ReadExi",
      "title": "ExiMiR function for reading Exiqon raw data into an AffyBatch object.",
      "topics": [
        "ReadExi"
      ]
    },
    {
      "page": "summarize.miR",
      "title": "ExiMiR low-level function for summarization.",
      "topics": [
        "summarize.miR"
      ]
    }
  ],
  "_rundeps": [
    "affy",
    "affyio",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "generics",
    "limma",
    "preprocessCore",
    "statmod"
  ],
  "_vignettes": [
    {
      "source": "ExiMiR-vignette.Rnw",
      "filename": "ExiMiR-vignette.pdf",
      "title": "Description of ExiMiR",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Raw and annotation data",
        "Raw data normalization",
        "Troubleshooting and fine-tuning options",
        "Concrete example with provided data",
        "Content of the file ''samplesinfo.txt''"
      ],
      "created": "2013-11-01 20:16:56",
      "modified": "2020-04-13 22:43:32",
      "commits": 4
    }
  ],
  "_score": 3.778151250383644,
  "_indexed": false,
  "_nocasepkg": "eximir",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/ExiMiR",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.54.0",
      "date": "2026-10-13T08:39:03.000Z",
      "distro": "resolute",
      "commit": "e275382de8434f98136da6c0ca69eba8db61b114",
      "fileid": "https://r2.ropensci.org/4b425d0951cd807101fa919151bc0d646a3709c04675a83af34083dd372a0f48",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38369713286"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.54.0",
      "date": "2026-10-13T08:37:17.000Z",
      "distro": "resolute",
      "commit": "e275382de8434f98136da6c0ca69eba8db61b114",
      "fileid": "https://r2.ropensci.org/ecdca663c14cdd1b5bba70c0814cecf8bdd2ee06e7430611dff885a7261d5cbe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38369713286"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.54.0",
      "date": "2026-10-13T08:50:51.000Z",
      "commit": "e275382de8434f98136da6c0ca69eba8db61b114",
      "fileid": "https://r2.ropensci.org/1881fe934fe45ebda6a4d18782315b815741477329f82b52ca71f12ad438f873",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38369713286"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.54.0",
      "date": "2026-10-13T08:49:38.000Z",
      "commit": "e275382de8434f98136da6c0ca69eba8db61b114",
      "fileid": "https://r2.ropensci.org/5da6c440baf1c921057d6a4b2b93451beba3d4c617da5941d07b165321de3a32",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38369713286"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.54.0",
      "date": "2026-10-13T08:36:24.000Z",
      "commit": "e275382de8434f98136da6c0ca69eba8db61b114",
      "fileid": "https://r2.ropensci.org/d6d8b279a789e67a327594fa88c6a0981f1837b44558577963e2ca69a25853c9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38369713286"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.54.0",
      "date": "2026-10-13T08:41:48.000Z",
      "commit": "e275382de8434f98136da6c0ca69eba8db61b114",
      "fileid": "https://r2.ropensci.org/1b6b0cb24e77c0827954de5afc08d03db33daa26e9e6c8fa0f33def6f7fd6ec4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38369713286"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.54.0",
      "date": "2026-10-13T08:40:42.000Z",
      "commit": "e275382de8434f98136da6c0ca69eba8db61b114",
      "fileid": "https://r2.ropensci.org/1e9122e26607b5196a5da464a7c1cd05df10174b8c41ae77be823ebe86122c1c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38369713286"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.54.0",
      "date": "2026-10-13T08:39:48.000Z",
      "commit": "e275382de8434f98136da6c0ca69eba8db61b114",
      "fileid": "https://r2.ropensci.org/9a7d4eafab832ed0846ef8bce4e7980aa674d5ce8d63876041ab0af17aaa0e3d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38369713286"
    }
  ]
}