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  "Date": "2025-07-22",
  "Type": "Package",
  "Title": "Operations on genomic intervals",
  "Author": "Julien Gagneur <gagneur@in.tum.de>, Joern Toedling, Richard\nBourgon, Nicolas Delhomme",
  "Maintainer": "Julien Gagneur <gagneur@in.tum.de>",
  "Description": "This package defines classes for representing genomic\nintervals and provides functions and methods for working with\nthese. Note: The package provides the basic infrastructure for\nand is enhanced by the package 'girafe'.",
  "License": "Artistic-2.0",
  "Collate": "AllGenerics.R Genome_intervals-class.R\nGenome_intervals-coercion-methods.R Genome_intervals-package.R\nGenome_intervals-ordering.R show-methods.R size-methods.R c.R\ncore_annotated.R distance_to_nearest-methods.R\ninterval_complement-methods.R interval_overlap-methods.R\ninterval_intersection-methods.R interval_union-methods.R\nwhich_nearest-methods.R parseGffAttributes.R readGff3.R\nwriteGff3.R",
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      "page": "genomeIntervals-package",
      "title": "Operations on genomic intervals",
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        "genomeIntervals"
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        "c,Genome_intervals-method",
        "c,Genome_intervals_stranded-method"
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    {
      "page": "core_annotated",
      "title": "Genome intervals with minimal annotation",
      "topics": [
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        "core_annotated,Genome_intervals-method",
        "core_annotated,Genome_intervals_stranded-method"
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    {
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      "title": "Distance in bases to the closest interval(s)",
      "topics": [
        "distance_to_nearest",
        "distance_to_nearest,Genome_intervals,Genome_intervals-method",
        "distance_to_nearest,Genome_intervals_stranded,Genome_intervals_stranded-method"
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        "j",
        "k"
      ]
    },
    {
      "page": "Genome_intervals-deprecated",
      "title": "The following function have been deprecated:         • 'seq_name'         • 'seq_name<-'",
      "topics": [
        "Genome_intervals deprecated functions",
        "seq_name",
        "seq_name,Genome_intervals-method",
        "seq_name<-",
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      "page": "Genome_intervals_stranded-class",
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      "topics": [
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        "Genome_intervals_stranded-class",
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        "strand,Genome_intervals_stranded-method",
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      "page": "Genome_intervals-class",
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        "annotation",
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        "coerce,Genome_intervals,data.frame-method",
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        "seqnames,Genome_intervals-method",
        "seqnames<-,Genome_intervals-method",
        "show,Genome_intervals-method",
        "size,Genome_intervals-method",
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        "type<-,Genome_intervals-method",
        "which_nearest,Genome_intervals,Genome_intervals-method",
        "width,Genome_intervals-method",
        "[,Genome_intervals,ANY-method",
        "[,Genome_intervals-method",
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        "[[,Genome_intervals,ANY,ANY-method",
        "[[,Genome_intervals,ANY-method",
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        "[[<-,Genome_intervals,ANY-method",
        "[[<-,Genome_intervals-method"
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    },
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      "page": "Genome_intervals-ordering",
      "title": "Ordering methods for Genome intervals",
      "topics": [
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        "order",
        "order,Genome_intervals-method",
        "order,Genome_intervals_stranded-method",
        "rank",
        "rank,Genome_intervals-method",
        "rank,Genome_intervals_stranded-method",
        "sort",
        "sort,Genome_intervals-method",
        "sort,Genome_intervals_stranded-method",
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        "xtfrm,Genome_intervals-method",
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      "title": "Constructor function for genomeIntervals objects",
      "topics": [
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        "GenomeIntervals-constructor"
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      "topics": [
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        "as,Genome_intervals,GRangesList-method",
        "as,Genome_intervals-method",
        "coerce,Genome_intervals,GRanges-method",
        "coerce,Genome_intervals,GRangesList-method",
        "genomeIntervals coercion methods"
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    },
    {
      "page": "getGffAttribute",
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      "topics": [
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