{
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  "Package": "GenomicFeatures",
  "Title": "Query the gene models of a given organism/assembly",
  "Description": "Extract the genomic locations of genes, transcripts,\nexons, introns, and CDS, for the gene models stored in a TxDb\nobject. A TxDb object is a small database that contains the\ngene models of a given organism/assembly. Bioconductor provides\na small collection of TxDb objects in the form of\nready-to-install TxDb packages for the most commonly studied\norganisms. Additionally, the user can easily make a TxDb object\n(or package) for the organism/assembly of their choice by using\nthe tools from the txdbmaker package.",
  "biocViews": "Genetics, Infrastructure, Annotation, Sequencing,\nGenomeAnnotation",
  "URL": "https://bioconductor.org/packages/GenomicFeatures",
  "BugReports": "https://github.com/Bioconductor/GenomicFeatures/issues",
  "Version": "1.65.0",
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  "Encoding": "UTF-8",
  "Authors@R": "c(\nperson(\"H.\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\"),\nperson(\"M.\", \"Carlson\", role=\"aut\"),\nperson(\"P.\", \"Aboyoun\", role=\"aut\"),\nperson(\"S.\", \"Falcon\", role=\"aut\"),\nperson(\"M.\", \"Morgan\", role=\"aut\"),\nperson(\"D.\", \"Sarkar\", role=\"aut\"),\nperson(\"M.\", \"Lawrence\", role=\"aut\"),\nperson(\"V.\", \"Obenchain\", role=\"aut\"),\nperson(\"S.\", \"Arora\", role=\"ctb\"),\nperson(\"J.\", \"MacDonald\", role=\"ctb\"),\nperson(\"M.\", \"Ramos\", role=\"ctb\"),\nperson(\"S.\", \"Saini\", role=\"ctb\"),\nperson(\"P.\", \"Shannon\", role=\"ctb\"),\nperson(\"L.\", \"Shepherd\", role=\"ctb\"),\nperson(\"D.\", \"Tenenbaum\", role=\"ctb\"),\nperson(\"D.\", \"Van Twisk\", role=\"ctb\"))",
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  "Collate": "utils.R TxDb-schema.R TxDb-SELECT-helpers.R TxDb-class.R\nFeatureDb-class.R mapIdsToRanges.R id2name.R transcripts.R\ntranscriptsBy.R transcriptsByOverlaps.R transcriptLengths.R\nexonicParts.R extendExonsIntoIntrons.R features.R tRNAs.R\nextractTranscriptSeqs.R extractUpstreamSeqs.R\ngetPromoterSeq-methods.R select-methods.R nearest-methods.R\ntranscriptLocs2refLocs.R coordinate-mapping-methods.R\nproteinToGenome.R coverageByTranscript.R zzz.R",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:15 UTC",
  "RemoteUrl": "https://github.com/bioc/GenomicFeatures",
  "RemoteRef": "HEAD",
  "RemoteSha": "41960e538fb4381917785e36762cded6118d66d1",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 19:40:38 UTC",
    "User": "root"
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  "Author": "H. Pagès [aut, cre],\nM. Carlson [aut],\nP. Aboyoun [aut],\nS. Falcon [aut],\nM. Morgan [aut],\nD. Sarkar [aut],\nM. Lawrence [aut],\nV. Obenchain [aut],\nS. Arora [ctb],\nJ. MacDonald [ctb],\nM. Ramos [ctb],\nS. Saini [ctb],\nP. Shannon [ctb],\nL. Shepherd [ctb],\nD. Tenenbaum [ctb],\nD. Van Twisk [ctb]",
  "Maintainer": "H. Pagès <hpages.on.github@gmail.com>",
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    "cds",
    "cdsBy",
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    "distance",
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    "extractTranscriptSeqs",
    "extractUpstreamSeqs",
    "features",
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    "getPromoterSeq",
    "getTerminatorSeq",
    "id2name",
    "intronicParts",
    "intronsByTranscript",
    "isActiveSeq",
    "isActiveSeq<-",
    "mapFromTranscripts",
    "mapIdsToRanges",
    "mapRangesToIds",
    "mapToTranscripts",
    "organism",
    "pcoverageByTranscript",
    "pmapFromTranscripts",
    "pmapToTranscripts",
    "promoters",
    "proteinToGenome",
    "seqinfo",
    "seqlevels<-",
    "seqlevels0",
    "show",
    "terminators",
    "threeUTRsByTranscript",
    "tidyExons",
    "tidyIntrons",
    "tidyTranscripts",
    "transcriptLengths",
    "transcriptLocs2refLocs",
    "transcripts",
    "transcriptsBy",
    "transcriptsByOverlaps",
    "transcriptWidths",
    "tRNAs"
  ],
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      "title": "Coerce to file format structures",
      "topics": [
        "asBED,TxDb-method",
        "asGFF,TxDb-method"
      ]
    },
    {
      "page": "coverageByTranscript",
      "title": "Compute coverage by transcript (or CDS) of a set of ranges",
      "topics": [
        "coverageByTranscript",
        "pcoverageByTranscript"
      ]
    },
    {
      "page": "exonicParts",
      "title": "Extract non-overlapping exonic or intronic parts from a TxDb-like object",
      "topics": [
        "exonicParts",
        "intronicParts",
        "tidyExons",
        "tidyIntrons",
        "tidyTranscripts"
      ]
    },
    {
      "page": "extendExonsIntoIntrons",
      "title": "Extend exons by a given number of bases into their adjacent introns",
      "topics": [
        "extendExonsIntoIntrons"
      ]
    },
    {
      "page": "extractTranscriptSeqs",
      "title": "Extract transcript (or CDS) sequences from chromosome sequences",
      "topics": [
        "extractTranscriptSeqs",
        "extractTranscriptSeqs,ANY-method",
        "extractTranscriptSeqs,DNAString-method"
      ]
    },
    {
      "page": "extractUpstreamSeqs",
      "title": "Extract sequences upstream of a set of genes or transcripts",
      "topics": [
        "extractUpstreamSeqs",
        "extractUpstreamSeqs,GenomicRanges-method",
        "extractUpstreamSeqs,GRangesList-method",
        "extractUpstreamSeqs,TxDb-method"
      ]
    },
    {
      "page": "FeatureDb-class",
      "title": "FeatureDb objects",
      "topics": [
        "class:FeatureDb",
        "FeatureDb",
        "FeatureDb-class"
      ]
    },
    {
      "page": "features",
      "title": "Extract simple features from a FeatureDb object",
      "topics": [
        "features",
        "features,FeatureDb-method"
      ]
    },
    {
      "page": "getPromoterSeq-methods",
      "title": "Get gene promoter or terminator sequences",
      "topics": [
        "getPromoterSeq",
        "getPromoterSeq,GRanges-method",
        "getPromoterSeq,GRangesList-method",
        "getTerminatorSeq",
        "getTerminatorSeq,GRanges-method",
        "getTerminatorSeq,GRangesList-method"
      ]
    },
    {
      "page": "id2name",
      "title": "Map internal ids to external names for a given feature type",
      "topics": [
        "id2name"
      ]
    },
    {
      "page": "mapIdsToRanges",
      "title": "Map IDs to Genomic Ranges",
      "topics": [
        "mapIdsToRanges",
        "mapIdsToRanges,TxDb-method"
      ]
    },
    {
      "page": "mapRangesToIds",
      "title": "Map Genomic Ranges to IDs",
      "topics": [
        "mapRangesToIds",
        "mapRangesToIds,TxDb-method"
      ]
    },
    {
      "page": "coordinate-mapping-methods",
      "title": "Map range coordinates between transcripts and genome space",
      "topics": [
        "coordinate-mapping",
        "coordinate-mapping-methods",
        "mapFromTranscripts",
        "mapFromTranscripts,GenomicRanges,GenomicRanges-method",
        "mapFromTranscripts,GenomicRanges,GRangesList-method",
        "mapToTranscripts",
        "mapToTranscripts,ANY,TxDb-method",
        "mapToTranscripts,GenomicRanges,GenomicRanges-method",
        "mapToTranscripts,GenomicRanges,GRangesList-method",
        "pmapFromTranscripts",
        "pmapFromTranscripts,GenomicRanges,GenomicRanges-method",
        "pmapFromTranscripts,GenomicRanges,GRangesList-method",
        "pmapFromTranscripts,IntegerRanges,GenomicRanges-method",
        "pmapFromTranscripts,IntegerRanges,GRangesList-method",
        "pmapToTranscripts",
        "pmapToTranscripts,GenomicRanges,GenomicRanges-method",
        "pmapToTranscripts,GenomicRanges,GRangesList-method",
        "pmapToTranscripts,GRangesList,GRangesList-method"
      ]
    },
    {
      "page": "nearest-methods",
      "title": "Finding the nearest genomic range neighbor in a TxDb",
      "topics": [
        "distance,GenomicRanges,TxDb-method",
        "nearest-methods"
      ]
    },
    {
      "page": "proteinToGenome",
      "title": "Map protein-relative coordinates to genomic coordinates",
      "topics": [
        "proteinToGenome",
        "proteinToGenome,ANY-method",
        "proteinToGenome,GRangesList-method"
      ]
    },
    {
      "page": "select-methods",
      "title": "Using the \"select\" interface on TxDb objects",
      "topics": [
        "columns,TxDb-method",
        "keys,TxDb-method",
        "keytypes,TxDb-method",
        "select,TxDb-method",
        "select-methods"
      ]
    },
    {
      "page": "transcriptLengths",
      "title": "Extract the transcript lengths (and other metrics) from a TxDb object",
      "topics": [
        "transcriptLengths"
      ]
    },
    {
      "page": "transcriptLocs2refLocs",
      "title": "Converting transcript-based locations into reference-based locations",
      "topics": [
        "transcriptLocs2refLocs",
        "transcriptWidths"
      ]
    },
    {
      "page": "transcripts",
      "title": "Extract genomic features from a TxDb-like object",
      "topics": [
        "cds",
        "cds,TxDb-method",
        "exons",
        "exons,TxDb-method",
        "genes",
        "genes,TxDb-method",
        "promoters",
        "promoters,TxDb-method",
        "terminators",
        "terminators,TxDb-method",
        "transcripts",
        "transcripts,TxDb-method"
      ]
    },
    {
      "page": "transcriptsBy",
      "title": "Extract and group genomic features of a given type from a TxDb-like object",
      "topics": [
        "cdsBy",
        "cdsBy,TxDb-method",
        "exonsBy",
        "exonsBy,TxDb-method",
        "fiveUTRsByTranscript",
        "fiveUTRsByTranscript,TxDb-method",
        "intronsByTranscript",
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      "title": "Obtaining and Utilizing TxDb Objects",
      "author": "Marc Carlson, Patrick Aboyoun, Hervé Pagès, Seth Falcon, Martin Morgan",
      "engine": "knitr::rmarkdown",
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        "Installing the GenomicFeatures package",
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        "Retrieving Data from a TxDb object",
        "Pre-filtering data based on Chromosomes",
        "Retrieving data using the select() method",
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