{ "_id": "6ae343bd327abcdf86867063", "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 ", "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": "2026-10-29 11:51:09 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "blima_1.47.0.tar.gz", "_fileid": "https://r2.ropensci.org/4877141fb166627839fb0c3aa237909871b83dc9d13354962c8d188e6e4aa92d", "_filesize": 454650, "_sha256": "4877141fb166627839fb0c3aa237909871b83dc9d13354962c8d188e6e4aa92d", "_expires": "2027-02-06T13:01:47.000Z", "_created": "2026-10-29T11:51:09.000Z", "_published": "2026-10-29T13:01:49.014Z", "_upstream": "https://github.com/bioc/blima", "_status": "success", "_maintainer": { "name": "Vojtěch Kulvait", "email": "kulvait@gmail.com", "login": "kulvait", "description": "Tomographic reconstruction, phase contrast imaging, visualization", "uuid": 2242196 }, "_jobs": [ { "job": 123429742608, "time": 199, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "12894434244" }, { "job": 123429742783, "time": 285, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "12895900178" }, { "job": 123429742493, "time": 314, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12894649202" }, { "job": 123429742578, "time": 271, "config": "linux-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12895640510" }, { "job": 123429742588, "time": 339, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12894938017" }, { "job": 123429742636, "time": 199, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "12899520259" }, { "job": 123429742602, "time": 350, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12898676632" }, { "job": 123429742666, "time": 231, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12898019822" }, { "job": 123429742658, "time": 572, "config": "macos-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12899141630" }, { "job": 123424044959, "time": 788, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12895305443" }, { "job": 123429742440, "time": 220, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12894373955" }, { "job": 123429742745, "time": 353, "config": "windows-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "12894743925" }, { "job": 123429742573, "time": 259, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12894733653" }, { "job": 123429742614, "time": 241, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12894638953" }, { "job": 123429742589, "time": 357, "config": "windows-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12896020022" }, { "job": 123429742723, "time": 192, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12894403625" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547", "_commit": { "id": "55531c04711c143f808c6469e43910799bf1755b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379948 }, "_distro": "resolute", "_host": "GitHub-Actions", "_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", "repository": "bioc" }, { "branch": "release", "version": "1.46.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "microarray", "preprocessing", "normalization", "differentialexpression", "generegulation", "geneexpression", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 481, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 683, "source": "https://www.bioconductor.org/packages/stats/bioc/blima" }, "_devurl": "https://bitbucket.org/kulvait/blima", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/blima.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_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", "BiocBaseUtils", "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": "16-20260322-1ubuntu1", "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": [ "1 Introduction", "2 Data annotation", "3 Background correction", "4 Variance Stabilizing Method", "5 Quantile normalization", "6 Data testing", "7 Summarization" ], "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": "2026-10-29T11:55:13.000Z", "distro": "resolute", "arch": "aarch64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/ec16c24cb868dda5d0a632d0280d5b8ab2a858d658f81cfe495555a50504c6ce", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-10-29T11:55:43.000Z", "distro": "resolute", "arch": "x86_64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/7188799ea194ea920674183a1834ed74e23a4159eb41d48743ee29ccdb553217", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.6.1", "os": "linux", "version": "1.47.0", "date": "2026-10-29T11:55:05.000Z", "distro": "resolute", "arch": "aarch64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/af5b28496a551683fb35ba6954bbe9deb8bfe46e8354bdeb1c502a41d3bef4e8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.6.1", "os": "linux", "version": "1.47.0", "date": "2026-10-29T11:56:14.000Z", "distro": "resolute", "arch": "x86_64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/55a335b5abd32919a9ada4f05a1733db43b7c9bc75176206b4ad509dd03252f7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-10-29T12:55:15.000Z", "arch": "aarch64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/8d8676e741b39ca13206629823541906ed866ab262bf7bbaa47d6ca60e74eb3c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-10-29T12:53:11.000Z", "arch": "x86_64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/6ed1bf047d47af868d0adebdac0065073308c3d36a5e5154fdec7afae44d9403", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.6.1", "os": "mac", "version": "1.47.0", "date": "2026-10-29T12:54:54.000Z", "arch": "aarch64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/b85ff2a23aff41eb560e7a40410d49628c5cd6b7377d05516a59288b88fb3f47", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.6.1", "os": "mac", "version": "1.47.0", "date": "2026-10-29T12:57:50.000Z", "arch": "x86_64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/c16b1216dad82e16ab41209da63b58f98c74fda67c5020d4943381f10a34ae68", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-10-29T11:55:18.000Z", "arch": "emscripten", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/cb00f2f75d3cf6f66bab8e1cff9f9718f66a9fb8d1dd31e96f8ae79e0849fa5d", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-10-29T11:55:52.000Z", "arch": "aarch64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/42b965f851ed96d3990ca061fc67b23a7a300a4d309d9a538a407312ee252275", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-10-29T11:53:42.000Z", "arch": "x86_64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/f630ca5879c1d41c2a2d2c6358ab3262b6eac371fb1b0e235529bf7cd86724db", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-10-29T11:53:58.000Z", "arch": "x86_64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/205586b510627285b57eae64e7385c98cef588b6bda3a99cc7b96d25509a6859", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.6.1", "os": "win", "version": "1.47.0", "date": "2026-10-29T11:56:08.000Z", "arch": "aarch64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/17a7a134d75a04f6e5960c91ceb71d3485585ca67774d02d2611f9ddab924bb1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" }, { "r": "4.6.1", "os": "win", "version": "1.47.0", "date": "2026-10-29T11:53:30.000Z", "arch": "x86_64", "commit": "55531c04711c143f808c6469e43910799bf1755b", "fileid": "https://r2.ropensci.org/cfbb3b1d76235345190feea3d1a5b6f2c36fb75cbe745a51c8691b2a3cd610f8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40866917547" } ] }