{
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  "Type": "Package",
  "Title": "BadRegionFinder: an R/Bioconductor package for identifying\nregions with bad coverage",
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  "Date": "2016-03-07",
  "Author": "Sarah Sandmann",
  "Maintainer": "Sarah Sandmann <sarah.sandmann@uni-muenster.de>",
  "Description": "BadRegionFinder is a package for identifying regions with\na bad, acceptable and good coverage in sequence alignment data\navailable as bam files. The whole genome may be considered as\nwell as a set of target regions. Various visual and textual\ntypes of output are available.",
  "License": "LGPL-3",
  "biocViews": "Coverage, Sequencing, Alignment, WholeGenome, Classification",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
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  "Date/Publication": "2026-04-28 12:43:12 UTC",
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  "_selfowned": false,
  "_usedby": 0,
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    "extra/citation.html",
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    "extra/contents.json",
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  "_realowner": "bioc",
  "_cranurl": false,
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    "determineCoverageQuality",
    "determineQuantiles",
    "determineRegionsOfInterest",
    "plotDetailed",
    "plotSummary",
    "plotSummaryGenes",
    "reportBadRegionsDetailed",
    "reportBadRegionsGenes",
    "reportBadRegionsSummary"
  ],
  "_help": [
    {
      "page": "BadRegionFinder-package",
      "title": "BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage",
      "topics": [
        "BadRegionFinder-package",
        "Bad Coverage",
        "BadRegionFinder",
        "Coverage Classifier"
      ]
    },
    {
      "page": "determineCoverage",
      "title": "Determines the coverage (recommended for whole-genome analyses)",
      "topics": [
        "determineCoverage"
      ]
    },
    {
      "page": "determineCoverageQuality",
      "title": "Classifies the determined coverage",
      "topics": [
        "determine Coverage Quality",
        "determineCoverageQuality"
      ]
    },
    {
      "page": "determineQuantiles",
      "title": "Determines basewise user-defined quantiles",
      "topics": [
        "determine Quantiles",
        "determineQuantiles"
      ]
    },
    {
      "page": "determineRegionsOfInterest",
      "title": "Determines the regions of interest",
      "topics": [
        "determine Regions Of Interest",
        "determineRegionsOfInterest"
      ]
    },
    {
      "page": "plotDetailed",
      "title": "Plots a more detailed overview of the coverage quality",
      "topics": [
        "plot Detailed",
        "plotDetailed"
      ]
    },
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      "page": "plotSummary",
      "title": "Plots a summary of the coverage quality",
      "topics": [
        "plot Summary",
        "plotSummary"
      ]
    },
    {
      "page": "plotSummaryGenes",
      "title": "Plots a summary of the coverage quality concerning the genes only",
      "topics": [
        "plot Summary Genes",
        "plotSummaryGenes"
      ]
    },
    {
      "page": "reportBadRegionsDetailed",
      "title": "Gives a detailed report on the coverage quality",
      "topics": [
        "report Bad Regions Detailed",
        "reportBadRegionsDetailed"
      ]
    },
    {
      "page": "reportBadRegionsGenes",
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      "topics": [
        "report Bad Regions Genes",
        "reportBadRegionsGenes"
      ]
    },
    {
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      "topics": [
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        "reportBadRegionsSummary"
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