{
  "_id": "6a194301acfb0bcc41dd7fef",
  "Package": "altcdfenvs",
  "Version": "2.74.0",
  "Title": "alternative CDF environments (aka probeset mappings)",
  "Author": "Laurent Gautier <lgautier@gmail.com>",
  "Maintainer": "Laurent Gautier <lgautier@gmail.com>",
  "biocViews": "Microarray, OneChannel, QualityControl, Preprocessing,\nAnnotation, ProprietaryPlatforms, Transcription",
  "Description": "Convenience data structures and functions to handle\ncdfenvs",
  "License": "GPL (>= 2)",
  "Collate": "appendCdfEnvAffy.R buildCdfEnv.matchprobes.R\nbuildCdfEnv.biostrings.R CdfEnv.R cdfenvs.R copyCdfEnvAffy.R\nreadFASTA.R removeIndex.R unique.CdfEnvAffy.R",
  "LazyLoad": "yes",
  "Packaged": {
    "Date": "2026-05-29 06:44:58 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:30:30 UTC",
  "RemoteUrl": "https://github.com/bioc/altcdfenvs",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "d1163abd3f6a1a905b2a4a9eb30f34f29f086adf",
  "NeedsCompilation": "no",
  "MD5sum": "f57e977d6ac3ffb67c749c694b482bca",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "altcdfenvs_2.74.0.tar.gz",
  "_fileid": "d43233355695cf0d07cd6bfe4ccbfc0baf549730a51da1d1f505b4b0474aded4",
  "_filesize": 472250,
  "_sha256": "d43233355695cf0d07cd6bfe4ccbfc0baf549730a51da1d1f505b4b0474aded4",
  "_created": "2026-05-29T06:44:58.000Z",
  "_published": "2026-05-29T07:40:49.895Z",
  "_jobs": [
    {
      "job": 78451752643,
      "time": 211,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7284788782"
    },
    {
      "job": 78451752684,
      "time": 270,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7284802410"
    },
    {
      "job": 78451752676,
      "time": 334,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7284817500"
    },
    {
      "job": 78451752674,
      "time": 138,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7285605527"
    },
    {
      "job": 78451752663,
      "time": 127,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7285599761"
    },
    {
      "job": 78451127015,
      "time": 313,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284737589"
    },
    {
      "job": 78451752671,
      "time": 173,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284779977"
    },
    {
      "job": 78451752736,
      "time": 488,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7284852442"
    },
    {
      "job": 78451752737,
      "time": 545,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7284867553"
    },
    {
      "job": 78451752705,
      "time": 479,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7284850221"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622378790",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/altcdfenvs",
  "_commit": {
    "id": "d1163abd3f6a1a905b2a4a9eb30f34f29f086adf",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379430
  },
  "_maintainer": {
    "name": "Laurent Gautier",
    "email": "lgautier@gmail.com",
    "login": "lgautier",
    "description": "Data Science, Life Sciences & Healthcare",
    "uuid": 650866
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.7",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "version": ">= 0.1.0",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.9.25",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "version": ">= 2.15.1",
      "role": "Depends"
    },
    {
      "package": "affy",
      "role": "Depends"
    },
    {
      "package": "makecdfenv",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "role": "Depends"
    },
    {
      "package": "hypergraph",
      "role": "Depends"
    },
    {
      "package": "plasmodiumanophelescdf",
      "role": "Suggests"
    },
    {
      "package": "hgu95acdf",
      "role": "Suggests"
    },
    {
      "package": "hgu133aprobe",
      "role": "Suggests"
    },
    {
      "package": "hgu133a.db",
      "role": "Suggests"
    },
    {
      "package": "hgu133acdf",
      "role": "Suggests"
    },
    {
      "package": "Rgraphviz",
      "role": "Suggests"
    },
    {
      "package": "RColorBrewer",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.75.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.74.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "onechannel",
    "qualitycontrol",
    "preprocessing",
    "annotation",
    "proprietaryplatforms",
    "transcription"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 568,
    "source": "https://www.bioconductor.org/packages/stats/bioc/altcdfenvs"
  },
  "_mentions": 5,
  "_searchresults": 6,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/altcdfenvs.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "appendCdfEnvAffy",
    "buildCdfEnv.biostrings",
    "buildCdfEnv.matchprobes",
    "copyCdfEnvAffy",
    "countduplicated",
    "countskip.FASTA.entries",
    "geneNames.CdfEnvAffy",
    "getCdfEnvAffy",
    "getxy.probeseq",
    "grep.FASTA.entry",
    "index2xy",
    "index2xy.CdfEnvAffy",
    "indexProbes.CdfEnvAffy",
    "matchAffyProbes",
    "mmProbes",
    "plot.CdfEnvAffy",
    "print.FASTA",
    "printValidCdfEnvAffy",
    "read.FASTA.entry",
    "read.n.FASTA.entries",
    "read.n.FASTA.entries.split",
    "read.n.FASTA.headers",
    "read.n.FASTA.sequences",
    "removeIndex",
    "skip.FASTA.entry",
    "toHypergraph",
    "unique.CdfEnvAffy",
    "validAffyBatch",
    "validCdfEnvAffy",
    "wrapCdfEnvAffy",
    "write.FASTA",
    "xy2index",
    "xy2index.CdfEnvAffy"
  ],
  "_datasets": [
    {
      "name": "cdfenvEx",
      "title": "CdfEnvAffy",
      "object": "cdfenvEx",
      "file": "cdfenvEx.rda",
      "class": [
        "CdfEnvAffy"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "AffyProbesMatch-class",
      "title": "Class \"AffyProbesMatch\"",
      "topics": [
        "AffyProbesMatch-class",
        "combine,AffyProbesMatch,AffyProbesMatch-method",
        "show,AffyProbesMatch-method",
        "toHypergraph,AffyProbesMatch-method"
      ]
    },
    {
      "page": "appendCdfEnvAffy",
      "title": "append probe sets to a CdfEnvAffy",
      "topics": [
        "appendCdfEnvAffy"
      ]
    },
    {
      "page": "buildCdfEnv.biostrings",
      "title": "Build CDF environments",
      "topics": [
        "buildCdfEnv.biostrings"
      ]
    },
    {
      "page": "CdfEnvAffy-class",
      "title": "Class \"CdfEnvAffy\"",
      "topics": [
        "CdfEnvAffy-class",
        "coerce,CdfEnvAffy,Cdf-method",
        "coerce,CdfEnvAffy,environment-method",
        "geneNames,CdfEnvAffy-method",
        "index2xy,CdfEnvAffy-method",
        "indexProbes,CdfEnvAffy,character-method",
        "plot,CdfEnvAffy,missing-method",
        "show,CdfEnvAffy-method",
        "toHypergraph,CdfEnvAffy-method",
        "xy2index,CdfEnvAffy-method",
        "[,CdfEnvAffy,character,missing,missing-method"
      ]
    },
    {
      "page": "cdfenvEx",
      "title": "CdfEnvAffy",
      "topics": [
        "cdfenvEx"
      ]
    },
    {
      "page": "cdfenv",
      "title": "functions related to cdfenvs",
      "topics": [
        "buildCdfEnv.matchprobes",
        "CdfEnv",
        "getCdfEnvAffy",
        "wrapCdfEnvAffy"
      ]
    },
    {
      "page": "copyCdfEnvAffy",
      "title": "make a copy of a CdfEnvAffy",
      "topics": [
        "copyCdfEnvAffy"
      ]
    },
    {
      "page": "countduplicated",
      "title": "Count the number of times probes are used",
      "topics": [
        "countduplicated"
      ]
    },
    {
      "page": "geneNames",
      "title": "get the names of the known probe sets",
      "topics": [
        "geneNames.CdfEnvAffy"
      ]
    },
    {
      "page": "getxy.probeseq",
      "title": "A function to get the XY coordinates from a probes sequences data frame",
      "topics": [
        "getxy.probeseq"
      ]
    },
    {
      "page": "index2xy",
      "title": "Functions to shuttle from indexes to XY coordinates",
      "topics": [
        "index2xy",
        "index2xy.CdfEnvAffy",
        "xy2index",
        "xy2index.CdfEnvAffy"
      ]
    },
    {
      "page": "indexProbes.CdfEnvAffy",
      "title": "indexes for probes",
      "topics": [
        "indexProbes.CdfEnvAffy"
      ]
    },
    {
      "page": "matchAffyProbes",
      "title": "Match the probes on an Affymetrix array",
      "topics": [
        "matchAffyProbes",
        "mmProbes"
      ]
    },
    {
      "page": "plot.CdfEnvAffy",
      "title": "A function to `plot' a CdfEnvAffy",
      "topics": [
        "plot.CdfEnvAffy"
      ]
    },
    {
      "page": "utils.FASTA",
      "title": "Functions to work with FASTA files / connections",
      "topics": [
        "countskip.FASTA.entries",
        "grep.FASTA.entry",
        "print.FASTA",
        "read.FASTA.entry",
        "read.n.FASTA.entries",
        "read.n.FASTA.entries.split",
        "read.n.FASTA.headers",
        "read.n.FASTA.sequences",
        "skip.FASTA.entry",
        "write.FASTA"
      ]
    },
    {
      "page": "removeIndex",
      "title": "A function to remove probes in an environment",
      "topics": [
        "removeIndex"
      ]
    },
    {
      "page": "toHypergraph",
      "title": "Transform to an hypergraph",
      "topics": [
        "toHypergraph"
      ]
    },
    {
      "page": "unique.CdfEnvAffy",
      "title": "Remove duplicated elements from a CdfEnvAffy",
      "topics": [
        "unique.CdfEnvAffy"
      ]
    },
    {
      "page": "validAffyBatch",
      "title": "Check validity of a CdfEnvAffy.",
      "topics": [
        "printValidCdfEnvAffy",
        "validAffyBatch",
        "validCdfEnvAffy"
      ]
    }
  ],
  "_rundeps": [
    "affy",
    "affyio",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "Biostrings",
    "crayon",
    "generics",
    "graph",
    "hypergraph",
    "IRanges",
    "makecdfenv",
    "preprocessCore",
    "S4Vectors",
    "Seqinfo",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "altcdfenvs.Rnw",
      "filename": "altcdfenvs.pdf",
      "title": "altcdfenvs",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 19:51:00",
      "modified": "2013-11-01 19:51:00",
      "commits": 1
    },
    {
      "source": "ngenomeschips.Rnw",
      "filename": "ngenomeschips.pdf",
      "title": "Alternative CDF environments for 2(or more)-genomes chips",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 19:51:00",
      "modified": "2019-02-25 12:57:32",
      "commits": 2
    },
    {
      "source": "modify.Rnw",
      "filename": "modify.pdf",
      "title": "Modifying existing CDF environments to make alternative CDF environments",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 19:51:00",
      "modified": "2019-02-25 12:57:32",
      "commits": 2
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": false,
  "_nocasepkg": "altcdfenvs",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/altcdfenvs",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.74.0",
      "date": "2026-05-29T06:48:43.000Z",
      "distro": "noble",
      "commit": "d1163abd3f6a1a905b2a4a9eb30f34f29f086adf",
      "fileid": "9d6eff4b5f3b3027c52379bd671756e6a9f818fbe9bc742754231428efc5d17a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622378790"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.74.0",
      "date": "2026-05-29T06:49:50.000Z",
      "distro": "noble",
      "commit": "d1163abd3f6a1a905b2a4a9eb30f34f29f086adf",
      "fileid": "5e1bbab3da8d371439b173956df389a6d56c5db2f8c5b371dcc357d60caa49b7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622378790"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.74.0",
      "date": "2026-05-29T07:39:48.000Z",
      "commit": "d1163abd3f6a1a905b2a4a9eb30f34f29f086adf",
      "fileid": "77976fcc469d6c9bd0861c7815bb6c5540b13b336f9517bc307e699745444cac",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622378790"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.74.0",
      "date": "2026-05-29T07:39:31.000Z",
      "commit": "d1163abd3f6a1a905b2a4a9eb30f34f29f086adf",
      "fileid": "612f8549c7de33afd9c760b1094752c15c0410e9f91870a89d791ac579897f68",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622378790"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.74.0",
      "date": "2026-05-29T06:48:18.000Z",
      "commit": "d1163abd3f6a1a905b2a4a9eb30f34f29f086adf",
      "fileid": "a22a280364c6341aab7bb4c26aaebcd3c0b5fa3df0f3a6d0694f50d887d967d0",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622378790"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.74.0",
      "date": "2026-05-29T06:52:17.000Z",
      "commit": "d1163abd3f6a1a905b2a4a9eb30f34f29f086adf",
      "fileid": "c450b83662b9c4d69a4128933dbbd58f135e5448f13ab2a70ea2d6a130064833",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622378790"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.74.0",
      "date": "2026-05-29T06:53:24.000Z",
      "commit": "d1163abd3f6a1a905b2a4a9eb30f34f29f086adf",
      "fileid": "7ab8fdc024656de964de2878804deea556396d55870392ed078b4ea1494795a1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622378790"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.74.0",
      "date": "2026-05-29T06:52:03.000Z",
      "commit": "d1163abd3f6a1a905b2a4a9eb30f34f29f086adf",
      "fileid": "95cba5a93ff4311d73fbac56fd7a81689b7d8c8ee5e741404e1b5a30682f732d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26622378790"
    }
  ]
}