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  "Package": "gDNAx",
  "Type": "Package",
  "Title": "Diagnostics for assessing genomic DNA contamination in RNA-seq\ndata",
  "Version": "1.11.0",
  "Authors@R": "c(\nperson(\"Beatriz\", \"Calvo-Serra\", email = \"beatriz.calvo@upf.edu\", role = c(\"aut\")),\nperson(\"Robert\", \"Castelo\", email = \"robert.castelo@upf.edu\", role = c(\"aut\", \"cre\")))",
  "Description": "Provides diagnostics for assessing genomic DNA\ncontamination in RNA-seq data, as well as plots representing\nthese diagnostics. Moreover, the package can be used to get an\ninsight into the strand library protocol used and, in case of\nstrand-specific libraries, the strandedness of the data.\nFurthermore, it provides functionality to filter out reads of\npotential gDNA origin.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "biocViews": "Transcription, Transcriptomics, RNASeq, Sequencing,\nPreprocessing, Software, GeneExpression, Coverage,\nDifferentialExpression, FunctionalGenomics, SplicedAlignment,\nAlignment",
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  "URL": "https://github.com/functionalgenomics/gDNAx",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:25 UTC",
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  "Author": "Beatriz Calvo-Serra [aut],\nRobert Castelo [aut, cre]",
  "Maintainer": "Robert Castelo <robert.castelo@upf.edu>",
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    "note": 10
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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        "gDNAx"
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      "title": "Filter alignments in a BAM file using a transcriptome",
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        "filterBAMtxFlag",
        "testBAMtxFlag"
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        "plot,gDNAx,ANY-method",
        "plotAlnOrigins",
        "plotFrgLength"
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        "allStrandModes,gDNAx-method",
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