{
  "_id": "6a1a14e51d7bb097a09ce4fd",
  "Package": "conumee",
  "Title": "Enhanced copy-number variation analysis using Illumina DNA\nmethylation arrays",
  "Version": "1.47.1",
  "Author": "Volker Hovestadt, Marc Zapatka",
  "Maintainer": "Volker Hovestadt <conumee@hovestadt.bio>",
  "Address": "Division of Molecular Genetics, German Cancer Research Center\n(DKFZ), Heidelberg, Germany",
  "Description": "This package contains a set of processing and plotting\nmethods for performing copy-number variation (CNV) analysis\nusing Illumina 450k or EPIC methylation arrays.",
  "License": "GPL (>= 2)",
  "LazyData": "false",
  "Collate": "classes.R annotation.R load.R process.R output.R data.R",
  "biocViews": "CopyNumberVariation, DNAMethylation, MethylationArray,\nMicroarray, Normalization, Preprocessing, QualityControl,\nSoftware",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "6.0.1",
  "Config/Bioconductor/UnsupportedPlatforms": "windows",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-29 18:37:22 UTC",
  "RemoteUrl": "https://github.com/bioc/conumee",
  "RemoteRef": "HEAD",
  "RemoteSha": "afd7c582f853c3bfe7f23522fb2cbd890886a930",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 22:07:20 UTC",
    "User": "root"
  },
  "MD5sum": "b63d5021fc1c3aceced3a27ec0fbec9e",
  "_user": "bioc",
  "_type": "src",
  "_file": "conumee_1.47.1.tar.gz",
  "_fileid": "912b084db76c85d327ffa7262dca2ba575bd5a97e00ce81978134ee0e454f6e0",
  "_filesize": 1230452,
  "_sha256": "912b084db76c85d327ffa7262dca2ba575bd5a97e00ce81978134ee0e454f6e0",
  "_created": "2026-05-29T22:07:20.000Z",
  "_published": "2026-05-29T22:36:21.239Z",
  "_jobs": [
    {
      "job": 78595548509,
      "time": 596,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7302219801"
    },
    {
      "job": 78595548471,
      "time": 1406,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7302396494"
    },
    {
      "job": 78595548450,
      "time": 1568,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7302430316"
    },
    {
      "job": 78595548488,
      "time": 1530,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7302422013"
    },
    {
      "job": 78595548531,
      "time": 1513,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7302418408"
    },
    {
      "job": 78593621742,
      "time": 964,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7302081500"
    },
    {
      "job": 78595548582,
      "time": 470,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7302191316"
    },
    {
      "job": 78595548505,
      "time": 1386,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7302392230"
    },
    {
      "job": 78595548554,
      "time": 1470,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7302410047"
    },
    {
      "job": 78595548499,
      "time": 1550,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7302426746"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26664144809",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/conumee",
  "_commit": {
    "id": "afd7c582f853c3bfe7f23522fb2cbd890886a930",
    "author": "A Wokaty <awokaty@users.noreply.github.com>",
    "committer": "A Wokaty <awokaty@users.noreply.github.com>",
    "message": "Bump version\n",
    "time": 1780079842
  },
  "_maintainer": {
    "name": "Volker Hovestadt",
    "email": "conumee@hovestadt.bio"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "minfi",
      "role": "Depends"
    },
    {
      "package": "IlluminaHumanMethylation450kanno.ilmn12.hg19",
      "role": "Depends"
    },
    {
      "package": "IlluminaHumanMethylation450kmanifest",
      "role": "Depends"
    },
    {
      "package": "IlluminaHumanMethylationEPICanno.ilm10b2.hg19",
      "role": "Depends"
    },
    {
      "package": "IlluminaHumanMethylationEPICmanifest",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "DNAcopy",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "minfiData",
      "role": "Suggests"
    },
    {
      "package": "RCurl",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-22",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.47.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.46.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "copynumbervariation",
    "dnamethylation",
    "methylationarray",
    "microarray",
    "normalization",
    "preprocessing",
    "qualitycontrol",
    "software"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 577,
    "source": "https://www.bioconductor.org/packages/stats/bioc/conumee"
  },
  "_mentions": 25,
  "_searchresults": 39,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/conumee.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CNV.bin",
    "CNV.create_anno",
    "CNV.detail",
    "CNV.detailplot",
    "CNV.detailplot_wrap",
    "CNV.fit",
    "CNV.genomeplot",
    "CNV.load",
    "CNV.process",
    "CNV.segment",
    "CNV.write",
    "read.450k.url",
    "show"
  ],
  "_datasets": [
    {
      "name": "detail_regions",
      "title": "detail_regions",
      "object": "detail_regions",
      "file": "detail_regions.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exclude_regions",
      "title": "exclude_regions",
      "object": "exclude_regions",
      "file": "exclude_regions.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "tcgaBRCA.sentrix2name",
      "title": "tcgaBRCA.sentrix2name",
      "object": "tcgaBRCA.sentrix2name",
      "file": "tcgaBRCA.sentrix2name.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "CNV.analysis-class",
      "title": "CNV.analysis class",
      "topics": [
        "CNV.analysis-class",
        "coef,CNV.analysis-method",
        "names,CNV.analysis-method",
        "names<-,CNV.analysis-method",
        "show,CNV.analysis-method"
      ]
    },
    {
      "page": "CNV.anno-class",
      "title": "CNV.anno class",
      "topics": [
        "CNV.anno-class",
        "show,CNV.anno-method"
      ]
    },
    {
      "page": "CNV.bin",
      "title": "CNV.bin",
      "topics": [
        "CNV.bin",
        "CNV.bin,CNV.analysis-method"
      ]
    },
    {
      "page": "CNV.check",
      "title": "CNV.check",
      "topics": [
        "CNV.check",
        "CNV.check,CNV.data-method"
      ]
    },
    {
      "page": "CNV.create_anno",
      "title": "CNV.create_anno",
      "topics": [
        "CNV.create_anno"
      ]
    },
    {
      "page": "CNV.create_bins",
      "title": "CNV.create_bins",
      "topics": [
        "CNV.create_bins"
      ]
    },
    {
      "page": "CNV.data-class",
      "title": "CNV.data class",
      "topics": [
        "CNV.data-class",
        "names,CNV.data-method",
        "names<-,CNV.data-method",
        "show,CNV.data-method",
        "[,CNV.data,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "CNV.detail",
      "title": "CNV.detail",
      "topics": [
        "CNV.detail",
        "CNV.detail,CNV.analysis-method"
      ]
    },
    {
      "page": "CNV.detailplot",
      "title": "CNV.detailplot",
      "topics": [
        "CNV.detailplot",
        "CNV.detailplot,CNV.analysis-method"
      ]
    },
    {
      "page": "CNV.detailplot_wrap",
      "title": "CNV.detailplot_wrap",
      "topics": [
        "CNV.detailplot_wrap",
        "CNV.detailplot_wrap,CNV.analysis-method"
      ]
    },
    {
      "page": "CNV.fit",
      "title": "CNV.fit",
      "topics": [
        "CNV.fit",
        "CNV.fit,CNV.data,CNV.data,CNV.anno-method"
      ]
    },
    {
      "page": "CNV.genomeplot",
      "title": "CNV.genomeplot",
      "topics": [
        "CNV.genomeplot",
        "CNV.genomeplot,CNV.analysis-method"
      ]
    },
    {
      "page": "CNV.load",
      "title": "CNV.load",
      "topics": [
        "CNV.load",
        "CNV.load,data.frame-method",
        "CNV.load,GenomicRatioSet-method",
        "CNV.load,matrix-method",
        "CNV.load,MethylSet-method",
        "CNV.load,numeric-method"
      ]
    },
    {
      "page": "CNV.merge_bins",
      "title": "CNV.merge_bins",
      "topics": [
        "CNV.merge_bins"
      ]
    },
    {
      "page": "CNV.process",
      "title": "CNV.process",
      "topics": [
        "CNV.process",
        "CNV.process,integer,integer,CNV.data,CNV.anno-method"
      ]
    },
    {
      "page": "CNV.segment",
      "title": "CNV.segment",
      "topics": [
        "CNV.segment",
        "CNV.segment,CNV.analysis-method"
      ]
    },
    {
      "page": "CNV.write",
      "title": "CNV.write",
      "topics": [
        "CNV.write",
        "CNV.write,CNV.analysis-method"
      ]
    },
    {
      "page": "detail_regions",
      "title": "detail_regions",
      "topics": [
        "detail_regions"
      ]
    },
    {
      "page": "exclude_regions",
      "title": "exclude_regions",
      "topics": [
        "exclude_regions"
      ]
    },
    {
      "page": "read.450k.url",
      "title": "read.450k.url",
      "topics": [
        "read.450k.url"
      ]
    },
    {
      "page": "tbl_ucsc",
      "title": "tbl_ucsc",
      "topics": [
        "tbl_ucsc"
      ]
    },
    {
      "page": "tcgaBRCA.sentrix2name",
      "title": "tcgaBRCA.sentrix2name",
      "topics": [
        "tcgaBRCA.sentrix2name"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/conumee/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "base64",
    "beanplot",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bumphunter",
    "cachem",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "dir.expiry",
    "DNAcopy",
    "doRNG",
    "dplyr",
    "fastmap",
    "filelock",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "genefilter",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GEOquery",
    "glue",
    "h5mread",
    "HDF5Array",
    "hms",
    "httr",
    "httr2",
    "IlluminaHumanMethylation450kanno.ilmn12.hg19",
    "IlluminaHumanMethylation450kmanifest",
    "IlluminaHumanMethylationEPICanno.ilm10b2.hg19",
    "IlluminaHumanMethylationEPICmanifest",
    "illuminaio",
    "IRanges",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mclust",
    "memoise",
    "mime",
    "minfi",
    "multtest",
    "nlme",
    "nor1mix",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "preprocessCore",
    "prettyunits",
    "progress",
    "purrr",
    "quadprog",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "readr",
    "rentrez",
    "reshape",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "rngtools",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "scrime",
    "selectr",
    "Seqinfo",
    "siggenes",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "conumee.Rmd",
      "filename": "conumee.html",
      "title": "The conumee vignette",
      "author": "Volker Hovestadt, Marc Zapatka (Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Load data",
        "Create annotation object",
        "Combine intensity values",
        "Perform CNV analysis",
        "Output plots and text files",
        "Contact & citation",
        "Session info",
        "References"
      ],
      "created": "2015-04-03 18:07:57",
      "modified": "2017-04-13 18:56:55",
      "commits": 3
    }
  ],
  "_score": 5.892094602690481,
  "_indexed": true,
  "_nocasepkg": "conumee",
  "_universes": [
    "bioc"
  ],
  "_previous": "1.47.0",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.47.1",
      "date": "2026-05-29T22:18:28.000Z",
      "distro": "noble",
      "commit": "afd7c582f853c3bfe7f23522fb2cbd890886a930",
      "fileid": "002aae9d66744c378f04ffff60b0e8acfa1e92b17b772e6a9890f6a5ee011e67",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664144809"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.47.1",
      "date": "2026-05-29T22:17:58.000Z",
      "distro": "noble",
      "commit": "afd7c582f853c3bfe7f23522fb2cbd890886a930",
      "fileid": "a204ea2e798ce7f73bf020b935543f9e58ceea177e4e43012fd1dd05ce7394a3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664144809"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.47.1",
      "date": "2026-05-29T22:14:15.000Z",
      "commit": "afd7c582f853c3bfe7f23522fb2cbd890886a930",
      "fileid": "131e0a49534e771e8bbdfbc498f43e65267de39094940ef41adc7372d8417045",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664144809"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.47.1",
      "date": "2026-05-29T22:15:53.000Z",
      "commit": "afd7c582f853c3bfe7f23522fb2cbd890886a930",
      "fileid": "a5b2dffa965c20568524af2e247b520f77d31a3170a708046bcc908471e5a5a6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664144809"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.47.1",
      "date": "2026-05-29T22:17:08.000Z",
      "commit": "afd7c582f853c3bfe7f23522fb2cbd890886a930",
      "fileid": "4937fa936bb9cc779ddc2a9faf1fbe6b4c3d6a39ee9ecab0450c05e4393a336d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664144809"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.47.1",
      "date": "2026-05-29T22:14:09.000Z",
      "commit": "afd7c582f853c3bfe7f23522fb2cbd890886a930",
      "fileid": "394c6558a633e96f561b0b2f57c9adaadcfe963be7d4bb87c05c7deb0b1ea189",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664144809"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.47.1",
      "date": "2026-05-29T22:14:09.000Z",
      "commit": "afd7c582f853c3bfe7f23522fb2cbd890886a930",
      "fileid": "f96d40e2d5ed9c674277e9259024e811002f20b97d88a62870b3ccaa145dd76b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664144809"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.47.1",
      "date": "2026-05-29T22:14:30.000Z",
      "commit": "afd7c582f853c3bfe7f23522fb2cbd890886a930",
      "fileid": "92431edca89c10ef06e777399eaa6ce6131a62e5c82d36fb6e1a7463e7b00a95",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664144809"
    }
  ]
}