{
  "_id": "6a1966f4acfb0bcc41de79d3",
  "Encoding": "UTF-8",
  "Package": "blima",
  "Type": "Package",
  "Title": "Tools for the preprocessing and analysis of the Illumina\nmicroarrays on the detector (bead) level",
  "Version": "1.47.0",
  "Date": "2017-09-23",
  "Author": "Vojtěch Kulvait",
  "Maintainer": "Vojtěch Kulvait <kulvait@gmail.com>",
  "Description": "Package blima includes several algorithms for the\npreprocessing of Illumina microarray data. It focuses to the\nbead level analysis and provides novel approach to the quantile\nnormalization of the vectors of unequal lengths. It provides\nvariety of the methods for background correction including\nbackground subtraction, RMA like convolution and background\noutlier removal. It also implements variance stabilizing\ntransformation on the bead level. There are also implemented\nmethods for data summarization. It also provides the methods\nfor performing T-tests on the detector (bead) level and on the\nprobe level for differential expression testing.",
  "License": "GPL-3",
  "LazyLoad": "yes",
  "URL": "https://bitbucket.org/kulvait/blima",
  "biocViews": "Microarray, Preprocessing, Normalization,\nDifferentialExpression, GeneRegulation, GeneExpression",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:39:08 UTC",
  "RemoteUrl": "https://github.com/bioc/blima",
  "RemoteRef": "HEAD",
  "RemoteSha": "55531c04711c143f808c6469e43910799bf1755b",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 08:29:16 UTC",
    "User": "root"
  },
  "MD5sum": "f867a67a0ab1393689f0d297bcb8f5e5",
  "_user": "bioc",
  "_type": "src",
  "_file": "blima_1.47.0.tar.gz",
  "_fileid": "6c062fcb42d24d8d85a23af5b04a4c9123a26790d1e002cfbec5b8e358242efe",
  "_filesize": 452963,
  "_sha256": "6c062fcb42d24d8d85a23af5b04a4c9123a26790d1e002cfbec5b8e358242efe",
  "_created": "2026-05-29T08:29:16.000Z",
  "_published": "2026-05-29T10:14:12.453Z",
  "_jobs": [
    {
      "job": 78465746140,
      "time": 295,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7286536019"
    },
    {
      "job": 78465746170,
      "time": 339,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286549622"
    },
    {
      "job": 78465746228,
      "time": 362,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286556405"
    },
    {
      "job": 78465746256,
      "time": 356,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286554500"
    },
    {
      "job": 78465746286,
      "time": 412,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286571175"
    },
    {
      "job": 78465746366,
      "time": 195,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7288301546"
    },
    {
      "job": 78465746167,
      "time": 327,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7287362119"
    },
    {
      "job": 78465746200,
      "time": 225,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7288318838"
    },
    {
      "job": 78465746159,
      "time": 491,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7287400890"
    },
    {
      "job": 78464400913,
      "time": 558,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286447386"
    },
    {
      "job": 78465746145,
      "time": 263,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286526878"
    },
    {
      "job": 78465746163,
      "time": 287,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286536160"
    },
    {
      "job": 78465746152,
      "time": 270,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7286528893"
    },
    {
      "job": 78465746183,
      "time": 347,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286551855"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 4,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/blima",
  "_commit": {
    "id": "55531c04711c143f808c6469e43910799bf1755b",
    "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": 1777379948
  },
  "_maintainer": {
    "name": "Vojtěch Kulvait",
    "email": "kulvait@gmail.com",
    "login": "kulvait",
    "description": "Tomographic reconstruction, phase contrast imaging, visualization",
    "uuid": 2242196
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "beadarray",
      "version": ">= 2.0.0",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "version": ">= 2.0.0",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.8",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "xtable",
      "role": "Suggests"
    },
    {
      "package": "blimaTestingData",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "illuminaHumanv4.db",
      "role": "Suggests"
    },
    {
      "package": "lumi",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.47.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.46.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "preprocessing",
    "normalization",
    "differentialexpression",
    "generegulation",
    "geneexpression",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 382,
    "source": "https://www.bioconductor.org/packages/stats/bioc/blima"
  },
  "_devurl": "https://bitbucket.org/kulvait/blima",
  "_searchresults": 3,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/blima.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_homeurl": "https://bitbucket.org/kulvait/blima",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bacgroundCorrect",
    "backgroundChannelSubtract",
    "chipArrayStatistics",
    "createSummarizedMatrix",
    "doProbeTTests",
    "doTTests",
    "log2TransformPositive",
    "nonPositiveCorrect",
    "plotBackgroundImageAfterCorrection",
    "plotBackgroundImageBeforeCorrection",
    "quantileNormalize",
    "selectedChannelTransform",
    "varianceBeadStabilise",
    "writeBackgroundImages",
    "xieBacgroundCorrect"
  ],
  "_help": [
    {
      "page": "blima-package",
      "title": "Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.",
      "topics": [
        "blima-package",
        "blima"
      ]
    },
    {
      "page": "aggregateAndPreprocess",
      "title": "Aggregate data",
      "topics": [
        "aggregateAndPreprocess"
      ]
    },
    {
      "page": "bacgroundCorrect",
      "title": "Data background correction.",
      "topics": [
        "bacgroundCorrect"
      ]
    },
    {
      "page": "bacgroundCorrectSingleArray",
      "title": "Data background correction.",
      "topics": [
        "bacgroundCorrectSingleArray"
      ]
    },
    {
      "page": "backgroundChannelSubtract",
      "title": "Background channel subtraction",
      "topics": [
        "backgroundChannelSubtract"
      ]
    },
    {
      "page": "backgroundChannelSubtractSingleArray",
      "title": "Background channel subtraction",
      "topics": [
        "backgroundChannelSubtractSingleArray"
      ]
    },
    {
      "page": "channelExistsIntegrityWithLogicalVectorList",
      "title": "Internal function",
      "topics": [
        "channelExistsIntegrityWithLogicalVectorList"
      ]
    },
    {
      "page": "checkIntegrity",
      "title": "Internal function",
      "topics": [
        "checkIntegrity"
      ]
    },
    {
      "page": "checkIntegrityLogical",
      "title": "Internal function",
      "topics": [
        "checkIntegrityLogical"
      ]
    },
    {
      "page": "checkIntegrityOfListOfBeadLevelDataObjects",
      "title": "Internal function",
      "topics": [
        "checkIntegrityOfListOfBeadLevelDataObjects"
      ]
    },
    {
      "page": "checkIntegrityOfSingleBeadLevelDataObject",
      "title": "Internal function",
      "topics": [
        "checkIntegrityOfSingleBeadLevelDataObject"
      ]
    },
    {
      "page": "chipArrayStatistics",
      "title": "Statistics of beadLevelData",
      "topics": [
        "chipArrayStatistics"
      ]
    },
    {
      "page": "createSummarizedMatrix",
      "title": "Summarized value matrix.",
      "topics": [
        "createSummarizedMatrix"
      ]
    },
    {
      "page": "doAction",
      "title": "Internal function",
      "topics": [
        "doAction"
      ]
    },
    {
      "page": "doProbeTTests",
      "title": "T-test for probe level data.",
      "topics": [
        "doProbeTTests"
      ]
    },
    {
      "page": "doTTests",
      "title": "T-test for bead (detector) level data.",
      "topics": [
        "doTTests"
      ]
    },
    {
      "page": "filterBg",
      "title": "Bg correct vector",
      "topics": [
        "filterBg"
      ]
    },
    {
      "page": "getNextVector",
      "title": "Support probe and beadl level testing.",
      "topics": [
        "getNextVector"
      ]
    },
    {
      "page": "initMeanDistribution",
      "title": "initMeanDistribution",
      "topics": [
        "initMeanDistribution"
      ]
    },
    {
      "page": "insertColumn",
      "title": "Internal function to support chipArrayStatistics",
      "topics": [
        "insertColumn"
      ]
    },
    {
      "page": "interpolateSortedVector",
      "title": "Interpolate sorted vector",
      "topics": [
        "interpolateSortedVector"
      ]
    },
    {
      "page": "interpolateSortedVectorRcpp_",
      "title": "interpolateSortedVectorRcpp",
      "topics": [
        "interpolateSortedVectorRcpp_"
      ]
    },
    {
      "page": "log2TransformPositive",
      "title": "Log2 transform of numbers >1.",
      "topics": [
        "log2TransformPositive"
      ]
    },
    {
      "page": "meanDistribution",
      "title": "Produce sorted double vector with mean distribution.",
      "topics": [
        "meanDistribution"
      ]
    },
    {
      "page": "nonParametricEstimator",
      "title": "INTERNAL FUNCTION Xie background correct.",
      "topics": [
        "nonParametricEstimator"
      ]
    },
    {
      "page": "nonPositiveCorrect",
      "title": "Correct non positive",
      "topics": [
        "nonPositiveCorrect"
      ]
    },
    {
      "page": "nonPositiveCorrectSingleArray",
      "title": "Correct non positive",
      "topics": [
        "nonPositiveCorrectSingleArray"
      ]
    },
    {
      "page": "numberOfDistributionElements",
      "title": "Internal",
      "topics": [
        "numberOfDistributionElements"
      ]
    },
    {
      "page": "performXieCorrection",
      "title": "INTERNAL FUNCTION Xie background correct.",
      "topics": [
        "performXieCorrection"
      ]
    },
    {
      "page": "plotBackgroundImageAfterCorrection",
      "title": "Plot background image after correction",
      "topics": [
        "plotBackgroundImageAfterCorrection"
      ]
    },
    {
      "page": "plotBackgroundImageBeforeCorrection",
      "title": "Plot background image before correction",
      "topics": [
        "plotBackgroundImageBeforeCorrection"
      ]
    },
    {
      "page": "quantileNormalize",
      "title": "Bead level quantile normalization.",
      "topics": [
        "quantileNormalize"
      ]
    },
    {
      "page": "readToVector",
      "title": "Support doTTests function.",
      "topics": [
        "readToVector"
      ]
    },
    {
      "page": "selectedChannelTransform",
      "title": "Channel transformation",
      "topics": [
        "selectedChannelTransform"
      ]
    },
    {
      "page": "selectedChannelTransformSingleArray",
      "title": "Channel transformation",
      "topics": [
        "selectedChannelTransformSingleArray"
      ]
    },
    {
      "page": "singleArrayNormalize",
      "title": "Bead level quantile normalization.",
      "topics": [
        "singleArrayNormalize"
      ]
    },
    {
      "page": "singleChannelExistsIntegrityWithLogicalVector",
      "title": "Internal function",
      "topics": [
        "singleChannelExistsIntegrityWithLogicalVector"
      ]
    },
    {
      "page": "singleCheckIntegrityLogicalVector",
      "title": "Internal function",
      "topics": [
        "singleCheckIntegrityLogicalVector"
      ]
    },
    {
      "page": "singleNumberOfDistributionElements",
      "title": "Internal",
      "topics": [
        "singleNumberOfDistributionElements"
      ]
    },
    {
      "page": "updateMeanDistribution",
      "title": "updateMeanDistribution",
      "topics": [
        "updateMeanDistribution"
      ]
    },
    {
      "page": "varianceBeadStabilise",
      "title": "Bead level VST.",
      "topics": [
        "varianceBeadStabilise"
      ]
    },
    {
      "page": "varianceBeadStabiliseSingleArray",
      "title": "Bead level VST.",
      "topics": [
        "varianceBeadStabiliseSingleArray"
      ]
    },
    {
      "page": "vstFromLumi",
      "title": "Function from LGPL lumi package 2.16.0",
      "topics": [
        "vstFromLumi"
      ]
    },
    {
      "page": "writeBackgroundImages",
      "title": "Write Background Images",
      "topics": [
        "writeBackgroundImages"
      ]
    },
    {
      "page": "xieBacgroundCorrect",
      "title": "Xie background correct.",
      "topics": [
        "xieBacgroundCorrect"
      ]
    },
    {
      "page": "xieBacgroundCorrectSingleArray",
      "title": "INTERNAL FUNCTION Xie background correct.",
      "topics": [
        "xieBacgroundCorrectSingleArray"
      ]
    }
  ],
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "beadarray",
    "BeadDataPackR",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "farver",
    "fastmap",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "hexbin",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lattice",
    "lifecycle",
    "limma",
    "magrittr",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "plyr",
    "png",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "statmod",
    "stringi",
    "stringr",
    "sys",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "blima.rnw",
      "filename": "blima.pdf",
      "title": "blima an R package for Bead Level Illumina Microarray Analysis",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2014-05-08 23:11:55",
      "modified": "2017-09-23 13:02:50",
      "commits": 5
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "blima",
  "_universes": [
    "bioc",
    "kulvait",
    "bitbucket-kulvait"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-05-29T08:34:06.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "ef5d398b02430a4969a863b4fccf7cd06cec2d42874b5668477b80c48d7a572d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-05-29T08:34:22.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "b0fb523bdec28fbc2a958b4b811955f551f9217ac0afebb21228cacbf82009fd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-05-29T08:34:25.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "3484357d59b8968b044940ee39b16b6cacdb52cf181ff1fb2a8aa256e54a0266",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-05-29T08:35:20.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "86774b7e3d046bb95ff3e68dd6775aada333f41d0aaffc5ec2fea6d5173d5024",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-05-29T10:11:52.000Z",
      "arch": "aarch64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "bea86d65dbe75dde2676fde91a14c98ab52609ae3dc1e4c66144556309054e38",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-05-29T09:18:39.000Z",
      "arch": "x86_64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "ebd6f9b71a36edde065231c912d6f3e02a90e83fc2ee59044ca4df7f4c45a1f0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-05-29T10:12:27.000Z",
      "arch": "aarch64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "69d9672942ad73355b1e100bda0c81d20a33bcf2b1983a9bc5e721e5cfbe192f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-05-29T09:20:22.000Z",
      "arch": "x86_64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "4c960c1d5896a84cc68835517940461caabd615601387839850d68cf497d33c1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.47.0",
      "date": "2026-05-29T08:34:07.000Z",
      "arch": "emscripten",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "8535d7b71061d0cbab2fe1de938d8ec118e9477ced45441996d41ef7a4265292",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-05-29T08:32:48.000Z",
      "arch": "x86_64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "74a13c97b2ee2d50bd56aaadb729aa6abb36e0b14dee4547dc13392e7d866507",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-05-29T08:32:25.000Z",
      "arch": "x86_64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "ee71ff471a042ebd6558263aee3e3061e1b0688354b737bc331c62d85584b912",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-05-29T08:33:16.000Z",
      "arch": "x86_64",
      "commit": "55531c04711c143f808c6469e43910799bf1755b",
      "fileid": "30027e2df44681b72498f79b81b7a0d3021fa7533009584f8e55ba5bcb50abd5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626463585"
    }
  ]
}