{
  "_id": "6abe475699f7aa8c6aa54ada",
  "Package": "ABarray",
  "Title": "Microarray QA and statistical data analysis for Applied\nBiosystems Genome Survey Microrarray (AB1700) gene expression\ndata.",
  "Version": "1.81.0",
  "Date": "2006-02-11",
  "Author": "Yongming Andrew Sun",
  "Maintainer": "Yongming Andrew Sun <sunya@appliedbiosystems.com>",
  "Description": "Automated pipline to perform gene expression analysis for\nApplied Biosystems Genome Survey Microarray (AB1700) data\nformat. Functions include data preprocessing, filtering,\ncontrol probe analysis, statistical analysis in one single\nfunction. A GUI interface is also provided. The raw data,\nprocessed data, graphics output and statistical results are\norganized into folders according to the analysis settings used.",
  "biocViews": "Microarray, OneChannel, Preprocessing",
  "License": "GPL",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:31:48 UTC",
  "RemoteUrl": "https://github.com/bioc/ABarray",
  "RemoteRef": "HEAD",
  "RemoteSha": "196750a1e836fd99b9daaa1641d5195203a1b019",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-01 11:33:31 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "ABarray_1.81.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d50bccdbeaa181d3301fb8a8c694adc646473a41b78784cf21ae175374d1ff3d",
  "_filesize": 603889,
  "_sha256": "d50bccdbeaa181d3301fb8a8c694adc646473a41b78784cf21ae175374d1ff3d",
  "_expires": "2027-01-09T11:43:15.000Z",
  "_created": "2026-10-01T11:33:31.000Z",
  "_published": "2026-10-01T11:43:18.003Z",
  "_bioccheck": {
    "error": 2,
    "warning": 2,
    "note": 13
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36855782418",
  "_status": "success",
  "_upstream": "https://github.com/bioc/ABarray",
  "_commit": {
    "id": "196750a1e836fd99b9daaa1641d5195203a1b019",
    "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": 1777379508
  },
  "_maintainer": {
    "name": "Yongming Andrew Sun",
    "email": "sunya@appliedbiosystems.com"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 110349006602,
      "time": 147,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11157888573"
    },
    {
      "job": 110349006724,
      "time": 234,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11158133656"
    },
    {
      "job": 110349006547,
      "time": 181,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11158128637"
    },
    {
      "job": 110349006762,
      "time": 107,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11157899535"
    },
    {
      "job": 110349006566,
      "time": 125,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11157754558"
    },
    {
      "job": 110347969218,
      "time": 184,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11157673417"
    },
    {
      "job": 110349006490,
      "time": 99,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11159112674"
    },
    {
      "job": 110349006697,
      "time": 117,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11157883579"
    },
    {
      "job": 110349006693,
      "time": 87,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11158462700"
    },
    {
      "job": 110349006644,
      "time": 79,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11157963402"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "multtest",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tcltk",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "LPE",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.81.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.80.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "onechannel",
    "preprocessing"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 471,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 704,
    "source": "https://www.bioconductor.org/packages/stats/bioc/ABarray"
  },
  "_mentions": 4,
  "_searchresults": 5,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/ABarray.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "ABarray",
    "ABarrayGUI",
    "calcsn",
    "concord",
    "cvv",
    "cvvPlot",
    "doANOVA",
    "doLPE",
    "doPlotEset",
    "doPlotFCT",
    "doVennDiagram",
    "drawVennDiagram",
    "getMemberEset",
    "getPantherMap",
    "hclusterPlot",
    "icpPlot",
    "imputeFlag",
    "lpe.fdr.BH",
    "mamaplot",
    "matrixPlot",
    "mvaPair2",
    "panel.cor",
    "panel.scatter",
    "qnNormalize",
    "rgcolorsfunc",
    "savejpg",
    "scaleColorBar",
    "snSummary"
  ],
  "_help": [
    {
      "page": "ABarray",
      "title": "Utility to perform QA, data transformation and statistical analysis",
      "topics": [
        "ABarray"
      ]
    },
    {
      "page": "ABarrayGUI",
      "title": "GUI for ABarray to perform QA, data transformation and statistical analysis",
      "topics": [
        "ABarrayGUI"
      ]
    },
    {
      "page": "calcsn",
      "title": "Calculate SN summary for each group",
      "topics": [
        "calcsn"
      ]
    },
    {
      "page": "concord",
      "title": "Calculate signal detection concordance",
      "topics": [
        "concord"
      ]
    },
    {
      "page": "cvv",
      "title": "CV calculation",
      "topics": [
        "cvv"
      ]
    },
    {
      "page": "cvvPlot",
      "title": "Plot CV value",
      "topics": [
        "cvvPlot"
      ]
    },
    {
      "page": "doANOVA",
      "title": "Perform one way or two way ANOVA",
      "topics": [
        "doANOVA"
      ]
    },
    {
      "page": "doLPE",
      "title": "Perform LPE analysis",
      "topics": [
        "doLPE"
      ]
    },
    {
      "page": "doPlotEset",
      "title": "Produce a number of QA plot plus t and ANOVA test",
      "topics": [
        "doPlotEset"
      ]
    },
    {
      "page": "doPlotFCT",
      "title": "Calculate fold change and t test, the plot",
      "topics": [
        "doPlotFCT"
      ]
    },
    {
      "page": "doVennDiagram",
      "title": "Create Venn Diagram",
      "topics": [
        "doVennDiagram"
      ]
    },
    {
      "page": "drawVennDiagram",
      "title": "Draw Venn Diagram",
      "topics": [
        "drawVennDiagram"
      ]
    },
    {
      "page": "getMemberEset",
      "title": "Produce a sub ExpressionSet given a group and its members",
      "topics": [
        "getMemberEset"
      ]
    },
    {
      "page": "getPantherMap",
      "title": "Create pie chart for probes involved in Panther Pathway",
      "topics": [
        "getPantherMap"
      ]
    },
    {
      "page": "hclusterPlot",
      "title": "heatmap generation",
      "topics": [
        "hclusterPlot"
      ]
    },
    {
      "page": "icpPlot",
      "title": "icp plot function",
      "topics": [
        "icpPlot"
      ]
    },
    {
      "page": "imputeFlag",
      "title": "Perform imputation for missing values (FLAG > 5000)",
      "topics": [
        "imputeFlag"
      ]
    },
    {
      "page": "lpe.fdr.BH",
      "title": "Perform FDR on LPE results",
      "topics": [
        "lpe.fdr.BH"
      ]
    },
    {
      "page": "mamaplot",
      "title": "MA plot function",
      "topics": [
        "mamaplot"
      ]
    },
    {
      "page": "matrixPlot",
      "title": "heatmap for matrix",
      "topics": [
        "matrixPlot"
      ]
    },
    {
      "page": "mvaPair2",
      "title": "plot MA for each pair of columns",
      "topics": [
        "mvaPair2"
      ]
    },
    {
      "page": "panel.cor",
      "title": "Create correlation panel",
      "topics": [
        "panel.cor"
      ]
    },
    {
      "page": "panel.scatter",
      "title": "Creat scatter plot",
      "topics": [
        "panel.scatter"
      ]
    },
    {
      "page": "qnNormalize",
      "title": "Perform quantile normalization",
      "topics": [
        "qnNormalize"
      ]
    },
    {
      "page": "rgcolorsfunc",
      "title": "generate color map",
      "topics": [
        "rgcolorsfunc"
      ]
    },
    {
      "page": "savejpg",
      "title": "save device to jpg image file",
      "topics": [
        "savejpg"
      ]
    },
    {
      "page": "scaleColorBar",
      "title": "Create scale for heatmap",
      "topics": [
        "scaleColorBar"
      ]
    },
    {
      "page": "snSummary",
      "title": "Create summary information for S/N ratio",
      "topics": [
        "snSummary"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "generics",
    "lattice",
    "MASS",
    "Matrix",
    "multtest",
    "survival"
  ],
  "_vignettes": [
    {
      "source": "ABarray.Rnw",
      "filename": "ABarray.pdf",
      "title": "ABarray gene expression",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 19:57:37",
      "modified": "2013-11-01 19:57:37",
      "commits": 1
    },
    {
      "source": "ABarrayGUI.Rnw",
      "filename": "ABarrayGUI.pdf",
      "title": "ABarray gene expression GUI interface",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 19:57:37",
      "modified": "2013-11-01 19:57:37",
      "commits": 1
    }
  ],
  "_score": 4.204119982655925,
  "_indexed": true,
  "_nocasepkg": "abarray",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.81.0",
      "date": "2026-10-01T11:37:02.000Z",
      "distro": "resolute",
      "commit": "196750a1e836fd99b9daaa1641d5195203a1b019",
      "fileid": "https://r2.ropensci.org/0269bf8a10f6571e374894a224b94d4180135ba5a01625045e20b38e9117259d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36855782418"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.81.0",
      "date": "2026-10-01T11:36:11.000Z",
      "distro": "resolute",
      "commit": "196750a1e836fd99b9daaa1641d5195203a1b019",
      "fileid": "https://r2.ropensci.org/8878580c74724097d008187ea0047b57e6a0ac9a8a7b27f9188609cf0fb06693",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36855782418"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.81.0",
      "date": "2026-10-01T11:42:09.000Z",
      "commit": "196750a1e836fd99b9daaa1641d5195203a1b019",
      "fileid": "https://r2.ropensci.org/7f5bcc6c839e613eb7c6492f772c3e4b0f9ab4b4f0580307bee9e8295bc3689f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36855782418"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.81.0",
      "date": "2026-10-01T11:42:08.000Z",
      "commit": "196750a1e836fd99b9daaa1641d5195203a1b019",
      "fileid": "https://r2.ropensci.org/a05e0bf6d3b9791c92432ec36a7399463221a5f8e5d27a1bf421a682ba4de065",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36855782418"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.81.0",
      "date": "2026-10-01T11:35:31.000Z",
      "commit": "196750a1e836fd99b9daaa1641d5195203a1b019",
      "fileid": "https://r2.ropensci.org/88522d5e90719a02e1ade2c4cbd7d47fd856dd4af33f4bfff0d845072c55f48f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36855782418"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.81.0",
      "date": "2026-10-01T11:34:56.000Z",
      "commit": "196750a1e836fd99b9daaa1641d5195203a1b019",
      "fileid": "https://r2.ropensci.org/74f98a838a7d7ca4cd9005afe8315cc58a475439f16faf94df82248b06dfdf5d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36855782418"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.81.0",
      "date": "2026-10-01T11:34:32.000Z",
      "commit": "196750a1e836fd99b9daaa1641d5195203a1b019",
      "fileid": "https://r2.ropensci.org/1f6246f27e9729fbc60b075b8d5adbc193944cf2faf286e9502d7b2ab426e826",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36855782418"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.81.0",
      "date": "2026-10-01T11:34:34.000Z",
      "commit": "196750a1e836fd99b9daaa1641d5195203a1b019",
      "fileid": "https://r2.ropensci.org/e8439457e6c9a2d27cd2fdae8e9b9f6e67c5dfd78e73c90ff8009fdd2973bdf9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36855782418"
    }
  ]
}