{
  "_id": "6ae75a4d1e2c7b3a4f530213",
  "Package": "codelink",
  "Version": "1.81.0",
  "Title": "Manipulation of Codelink microarray data",
  "Author": "Diego Diez",
  "Maintainer": "Diego Diez <diego10ruiz@gmail.com>",
  "LazyLoad": "yes",
  "Description": "This package facilitates reading, preprocessing and\nmanipulating Codelink microarray data. The raw data must be\nexported as text file using the Codelink software.",
  "License": "GPL-2",
  "Collate": "Codelink-class.R CodelinkSet-class.R file.R data.R norm.R\nplot.R CodelinkSet-methods.R CodelinkSet-tools.R\nCodelinkSetUnique-class.R CodelinkSetUnique-methods.R filter.R\ncluster.R",
  "biocViews": "Microarray, OneChannel, DataImport, Preprocessing",
  "ByteCompile": "yes",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/ddiez/codelink",
  "BugReports": "https://github.com/ddiez/codelink/issues",
  "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:31:34 UTC",
  "RemoteUrl": "https://github.com/bioc/codelink",
  "RemoteRef": "HEAD",
  "RemoteSha": "fb0f534aa37ae95eb0b1072f2387e59ef8ff535e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 13:25:47 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "codelink_1.81.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/35df0af9e39622f44bf670ef297089e19b7279a97342a2575caed10ca8011c5f",
  "_filesize": 3492635,
  "_sha256": "35df0af9e39622f44bf670ef297089e19b7279a97342a2575caed10ca8011c5f",
  "_expires": "2027-02-09T15:27:07.000Z",
  "_created": "2026-11-01T13:25:47.000Z",
  "_published": "2026-11-01T15:27:09.135Z",
  "_upstream": "https://github.com/bioc/codelink",
  "_status": "success",
  "_maintainer": {
    "name": "Diego Diez",
    "email": "diego10ruiz@gmail.com",
    "login": "ddiez",
    "description": "Computational biologist working on immunology",
    "uuid": 3292149
  },
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    "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",
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  "_contributors": [
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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      {
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    ],
    "imports": [
      {
        "key": "Biobase::ExpressionSet",
        "hash": "977be3a5f37731d2"
      },
      {
        "key": "Biobase::Versioned",
        "hash": "85bb92eb18e2854f"
      },
      {
        "key": "Biobase::VersionedBiobase",
        "hash": "13a8ac2c79a1328e"
      },
      {
        "key": "Biobase::eSet",
        "hash": "f5a727537605d4e0"
      },
      {
        "key": "Biobase::generic:exprs",
        "hash": "d6308eaa8a6acdf7"
      },
      {
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        "hash": "251ab50a7be69eb9"
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/codelink.html",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_homeurl": "https://github.com/ddiez/codelink",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "annotation",
    "arrayNew",
    "averageProbes",
    "bkgdCorrect",
    "chipDevice",
    "codCorrect",
    "Codelink2CodelinkSet",
    "codNormalize",
    "codPlot",
    "codPreprocess",
    "codUniverse",
    "createWeights",
    "cutCV",
    "exprs",
    "fc2Cond",
    "filterSNR",
    "getBkg",
    "getFlag",
    "getInfo",
    "getInt",
    "getSNR",
    "getWeight",
    "imageCodelink",
    "logCodelink",
    "meanSNR",
    "mergeArray",
    "na2false",
    "normalize",
    "plotCorrelation",
    "plotCV",
    "plotDensities",
    "plotMA",
    "probeNames",
    "probeTypes",
    "readCodelink",
    "readCodelinkSet",
    "reportCodelink",
    "selCV",
    "show",
    "summary",
    "summaryFlag",
    "writeCluster",
    "writeCodelink"
  ],
  "_datasets": [
    {
      "name": "codelink.example",
      "title": "Dataset of class 'Codelink'",
      "object": "codelink.example",
      "file": "codelink.example.rda",
      "class": [
        "Codelink"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "codset",
      "title": "Dataset of class 'CodelinkSet'",
      "object": "codset",
      "file": "codset.rda",
      "class": [
        "CodelinkSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "arrayNew",
      "title": "Create a new x11 device",
      "topics": [
        "arrayNew"
      ]
    },
    {
      "page": "arraySize",
      "title": "Determine the size of the array",
      "topics": [
        "arraySize"
      ]
    },
    {
      "page": "as.matrix.Codelink",
      "title": "Return a matrix of intensity values",
      "topics": [
        "as.matrix.Codelink"
      ]
    },
    {
      "page": "averageProbes",
      "title": "averageProbes",
      "topics": [
        "averageProbes",
        "averageProbes,CodelinkSet-method"
      ]
    },
    {
      "page": "bkgdCorrect",
      "title": "Background correction of intensity values.",
      "topics": [
        "bkgdCorrect",
        "codCorrect",
        "codCorrect,CodelinkSet-method"
      ]
    },
    {
      "page": "Codelink-class",
      "title": "Class Codelink",
      "topics": [
        "class:Codelink",
        "Codelink",
        "Codelink-class",
        "show,Codelink-method",
        "[,Codelink,ANY,ANY-method",
        "[,Codelink-method"
      ]
    },
    {
      "page": "codelink.example",
      "title": "Dataset of class 'Codelink'",
      "topics": [
        "codelink.example"
      ]
    },
    {
      "page": "CodelinkSet-class",
      "title": "Class CodelinkSet",
      "topics": [
        "class::CodelinkSet",
        "Codelink2CodelinkSet",
        "CodelinkSet",
        "CodelinkSet-class",
        "codPreprocess",
        "codPreprocess,CodelinkSet-method",
        "exprs,CodelinkSet-method",
        "getBkg",
        "getBkg,CodelinkSet-method",
        "getFlag",
        "getFlag,CodelinkSet-method",
        "getInfo",
        "getInfo,CodelinkSet-method",
        "getInt",
        "getInt,CodelinkSet-method",
        "getSNR",
        "getSNR,CodelinkSet-method",
        "getWeight",
        "getWeight,CodelinkSet-method",
        "probeNames",
        "probeNames,CodelinkSet-method",
        "probeNames,CodelinkSetUnique-method",
        "probeTypes",
        "probeTypes,CodelinkSet-method"
      ]
    },
    {
      "page": "CodelinkSetUnique-class",
      "title": "Class CodelinkSetUnique",
      "topics": [
        "class::CodelinkSetUnique",
        "CodelinkSetUnique",
        "CodelinkSetUnique-class"
      ]
    },
    {
      "page": "codPlot",
      "title": "Diagnostic plots for CodelinkSet object.",
      "topics": [
        "codPlot",
        "codPlot,CodelinkSet-method",
        "codPlot,MArrayLM-method"
      ]
    },
    {
      "page": "codset",
      "title": "Dataset of class 'CodelinkSet'",
      "topics": [
        "codset"
      ]
    },
    {
      "page": "createWeights",
      "title": "Create weight for Codelink chips",
      "topics": [
        "createWeights",
        "createWeights,Codelink-method",
        "createWeights,CodelinkSet-method"
      ]
    },
    {
      "page": "cutCV",
      "title": "Calculate cutoff based in CV.",
      "topics": [
        "cutCV"
      ]
    },
    {
      "page": "decDetect",
      "title": "Determine decimal type of Codelink files",
      "topics": [
        "decDetect"
      ]
    },
    {
      "page": "dim.Codelink",
      "title": "Return the dimension of a Codelink object.",
      "topics": [
        "dim.Codelink"
      ]
    },
    {
      "page": "fc2Cond",
      "title": "Select probes based on fold change calculation",
      "topics": [
        "fc2Cond"
      ]
    },
    {
      "page": "imageCodelink",
      "title": "Image plot of Codelink arrays",
      "topics": [
        "imageCodelink"
      ]
    },
    {
      "page": "logCodelink",
      "title": "Application of logCodelink to Codelink object",
      "topics": [
        "logCodelink"
      ]
    },
    {
      "page": "mergeArray",
      "title": "Merge Codelink Bioarrays Data",
      "topics": [
        "mergeArray"
      ]
    },
    {
      "page": "na2false",
      "title": "Set NAs to FALSE",
      "topics": [
        "na2false"
      ]
    },
    {
      "page": "normalize",
      "title": "Normalization wrapper for Codelink/CodelinkSet objects.",
      "topics": [
        "codNormalize",
        "codNormalize,CodelinkSet-method",
        "normalize",
        "normalize,Codelink-method",
        "normalize,CodelinkSet-method"
      ]
    },
    {
      "page": "plotCorrelation",
      "title": "Plot correlation scatterplot between two arrays",
      "topics": [
        "plotCorrelation"
      ]
    },
    {
      "page": "plotCV",
      "title": "Plot of CV",
      "topics": [
        "plotCV"
      ]
    },
    {
      "page": "plotDensities",
      "title": "Plot Densities",
      "topics": [
        "plotDensities",
        "plotDensities,Codelink-method"
      ]
    },
    {
      "page": "plotMA",
      "title": "MA plot",
      "topics": [
        "plotMA"
      ]
    },
    {
      "page": "printHead",
      "title": "Print briefly a Codelink object",
      "topics": [
        "printHead"
      ]
    },
    {
      "page": "readCodelink",
      "title": "Read Codelink Bioarrays Data",
      "topics": [
        "readCodelink",
        "readCodelinkSet"
      ]
    },
    {
      "page": "readHeader",
      "title": "Read Header from Codelink Bioarrays Files",
      "topics": [
        "readHeader"
      ]
    },
    {
      "page": "readHeaderXLS",
      "title": "Read Header from XLS exported Codelink Bioarrays Files",
      "topics": [
        "readHeaderXLS"
      ]
    },
    {
      "page": "reportCodelink",
      "title": "Write a report of genes selected in HTML",
      "topics": [
        "reportCodelink"
      ]
    },
    {
      "page": "selCV",
      "title": "Select based on CV cutoff.",
      "topics": [
        "selCV"
      ]
    },
    {
      "page": "SNR",
      "title": "Calculate SNR",
      "topics": [
        "SNR"
      ]
    },
    {
      "page": "writeCodelink",
      "title": "Write a Codelink object to file.",
      "topics": [
        "writeCodelink",
        "writeCodelink,CodelinkSet-method"
      ]
    }
  ],
  "_rundeps": [
    "annotate",
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "fastmap",
    "generics",
    "glue",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lifecycle",
    "limma",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "statmod",
    "sys",
    "vctrs",
    "XML",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
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      "source": "Codelink_Introduction.Rnw",
      "filename": "Codelink_Introduction.pdf",
      "title": "Codelink Intruction",
      "engine": "knitr",
      "headings": [],
      "created": "2013-08-15 08:47:16",
      "modified": "2013-10-23 14:04:33",
      "commits": 9
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    {
      "source": "Codelink_Legacy.Rnw",
      "filename": "Codelink_Legacy.pdf",
      "title": "Codelink Legacy",
      "engine": "knitr",
      "headings": [],
      "created": "2013-08-15 08:47:16",
      "modified": "2013-10-23 14:04:33",
      "commits": 8
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  "_indexed": true,
  "_nocasepkg": "codelink",
  "_universes": [
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