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  "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",
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  "Date/Publication": "2026-04-28 12:30:30 UTC",
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    "extra/contents.json",
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    "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"
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      "title": "CdfEnvAffy",
      "object": "cdfenvEx",
      "file": "cdfenvEx.rda",
      "class": [
        "CdfEnvAffy"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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      "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"
      ]
    },
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      "page": "utils.FASTA",
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        "read.n.FASTA.entries",
        "read.n.FASTA.entries.split",
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        "read.n.FASTA.sequences",
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      ]
    },
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      ]
    },
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      "title": "Transform to an hypergraph",
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      ]
    },
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      "title": "Check validity of a CdfEnvAffy.",
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        "validAffyBatch",
        "validCdfEnvAffy"
      ]
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