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  "Package": "plyranges",
  "Type": "Package",
  "Title": "A fluent interface for manipulating GenomicRanges",
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  "Authors@R": "c(\nperson(\"Stuart\", \"Lee\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-1179-8436\")),\nperson(\"Michael\", \"Lawrence\", role = c(\"aut\", \"ctb\")),\nperson(\"Dianne\", \"Cook\", role = c(\"aut\", \"ctb\")),\nperson(\"Spencer\", \"Nystrom\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-1000-1579\")),\nperson(\"Pierre-Paul\", \"Axisa\", role=c(\"ctb\")),\nperson(\"Michael\", \"Love\", role = c(\"ctb\",\"cre\"),\nemail = \"michaelisaiahlove@gmail.com\")\n)",
  "Maintainer": "Michael Love <michaelisaiahlove@gmail.com>",
  "Description": "A dplyr-like interface for interacting with the common\nBioconductor classes Ranges and GenomicRanges. By providing a\ngrammatical and consistent way of manipulating these classes\ntheir accessiblity for new Bioconductor users is hopefully\nincreased.",
  "URL": "https://tidyomics.github.io/plyranges",
  "biocViews": "Infrastructure, DataRepresentation, WorkflowStep, Coverage",
  "BugReports": "https://github.com/tidyomics/plyranges",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:38 UTC",
  "RemoteUrl": "https://github.com/bioc/plyranges",
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  "Author": "Stuart Lee [aut] (ORCID: <https://orcid.org/0000-0003-1179-8436>),\nMichael Lawrence [aut, ctb],\nDianne Cook [aut, ctb],\nSpencer Nystrom [ctb] (ORCID: <https://orcid.org/0000-0003-1000-1579>),\nPierre-Paul Axisa [ctb],\nMichael Love [ctb, cre]",
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    "add_nearest_distance",
    "add_nearest_distance_downstream",
    "add_nearest_distance_left",
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    "anchor_5p",
    "anchor_center",
    "anchor_centre",
    "anchor_end",
    "anchor_start",
    "as_granges",
    "as_iranges",
    "as_ranges",
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    "bind_ranges",
    "chop_by_gaps",
    "chop_by_introns",
    "complement_ranges",
    "complement_ranges_directed",
    "compute_coverage",
    "count_overlaps",
    "count_overlaps_directed",
    "count_overlaps_within",
    "count_overlaps_within_directed",
    "disjoin_ranges",
    "disjoin_ranges_directed",
    "expand_ranges",
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    "filter_by_non_overlaps_directed",
    "filter_by_overlaps",
    "filter_by_overlaps_directed",
    "find_overlaps",
    "find_overlaps_directed",
    "find_overlaps_within",
    "find_overlaps_within_directed",
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    "flank_left",
    "flank_right",
    "flank_upstream",
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    "get_genome_info",
    "group_by_overlaps",
    "id_to_column",
    "intersect_ranges",
    "intersect_ranges_directed",
    "interweave",
    "join_follow",
    "join_follow_left",
    "join_follow_upstream",
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    "join_nearest_downstream",
    "join_nearest_left",
    "join_nearest_right",
    "join_nearest_upstream",
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    "join_overlap_inner_directed",
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    "join_overlap_intersect_directed",
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    "join_overlap_left_within_directed",
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    "join_overlap_self_within",
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    "join_precede_downstream",
    "join_precede_right",
    "n",
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    "names_to_column",
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      "title": "plyranges: a grammar of genomic data manipulation",
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        "plyranges-package",
        "plyranges"
      ]
    },
    {
      "page": "element-setops",
      "title": "Row-wise set operations on Ranges objects",
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        "%setdiff%",
        "%union%",
        "between",
        "span"
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        "add_nearest_distance_right",
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        "anchor_3p",
        "anchor_5p",
        "anchor_center",
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        "anchor_end",
        "anchor_start",
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      "topics": [
        "arrange.Ranges"
      ]
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        "as_iranges"
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      "topics": [
        "as_ranges"
      ]
    },
    {
      "page": "ranges-bind",
      "title": "Combine Ranges by concatentating them together",
      "topics": [
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        "chop_by_introns"
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      "topics": [
        "compute_coverage"
      ]
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      "title": "Count the number of overlaps between two Ranges objects",
      "topics": [
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        "count_overlaps.GenomicRanges",
        "count_overlaps.IntegerRanges",
        "count_overlaps_directed",
        "count_overlaps_directed.GenomicRanges",
        "count_overlaps_within",
        "count_overlaps_within.GenomicRanges",
        "count_overlaps_within.IntegerRanges",
        "count_overlaps_within_directed",
        "count_overlaps_within_directed.GenomicRanges"
      ]
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    {
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      "topics": [
        "DeferredGenomicRanges-class"
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    },
    {
      "page": "ranges-disjoin",
      "title": "Disjoin then aggregate a Ranges object",
      "topics": [
        "disjoin_ranges",
        "disjoin_ranges_directed"
      ]
    },
    {
      "page": "ranges-expand",
      "title": "Expand list-columns in a Ranges object",
      "topics": [
        "expand_ranges"
      ]
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      "page": "ranges-class",
      "title": "An abstract class to represent operations performed over a file",
      "topics": [
        "BamFileOperator-class",
        "FileOperator-class"
      ]
    },
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        "filter_by_non_overlaps_directed",
        "filter_by_overlaps",
        "filter_by_overlaps_directed"
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    {
      "page": "filter-ranges",
      "title": "Subset a 'Ranges' object",
      "topics": [
        "filter-ranges",
        "filter.Ranges"
      ]
    },
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      "title": "Find overlap between two Ranges",
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        "find_overlaps",
        "find_overlaps.GenomicRanges",
        "find_overlaps.IntegerRanges",
        "find_overlaps_directed",
        "find_overlaps_directed.GenomicRanges",
        "find_overlaps_within",
        "find_overlaps_within.GenomicRanges",
        "find_overlaps_within.IntegerRanges",
        "find_overlaps_within_directed",
        "find_overlaps_within_directed.GenomicRanges",
        "group_by_overlaps",
        "group_by_overlaps.GenomicRanges",
        "group_by_overlaps.IntegerRanges"
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    },
    {
      "page": "ranges-flank",
      "title": "Generate flanking regions",
      "topics": [
        "flank_downstream",
        "flank_left",
        "flank_right",
        "flank_upstream"
      ]
    },
    {
      "page": "group_by-ranges",
      "title": "Group a Ranges by one or more variables",
      "topics": [
        "GroupedGenomicRanges-class",
        "GroupedIntegerRanges-class",
        "groups.GroupedGenomicRanges",
        "groups.GroupedIntegerRanges",
        "group_by-ranges",
        "group_by.GenomicRanges",
        "ungroup.GroupedGenomicRanges"
      ]
    },
    {
      "page": "ranges-setops",
      "title": "Vector-wise Range set-operations",
      "topics": [
        "complement_ranges",
        "complement_ranges_directed",
        "intersect_ranges",
        "intersect_ranges_directed",
        "setdiff_ranges",
        "setdiff_ranges_directed",
        "union_ranges",
        "union_ranges_directed"
      ]
    },
    {
      "page": "ranges-interweave",
      "title": "Interweave a pair of Ranges objects together",
      "topics": [
        "interweave"
      ]
    },
    {
      "page": "ranges-follow",
      "title": "Find following Ranges",
      "topics": [
        "join_follow",
        "join_follow_left",
        "join_follow_upstream"
      ]
    },
    {
      "page": "mcols-joins",
      "title": "Join data by metadata columns",
      "topics": [
        "join_mcols_inner",
        "join_mcols_left"
      ]
    },
    {
      "page": "ranges-nearest",
      "title": "Find nearest neighbours between two Ranges objects",
      "topics": [
        "join_nearest",
        "join_nearest_downstream",
        "join_nearest_left",
        "join_nearest_right",
        "join_nearest_upstream"
      ]
    },
    {
      "page": "overlap-joins",
      "title": "Join by overlapping Ranges",
      "topics": [
        "join_overlap_inner",
        "join_overlap_inner_directed",
        "join_overlap_inner_within",
        "join_overlap_inner_within_directed",
        "join_overlap_intersect",
        "join_overlap_intersect_directed",
        "join_overlap_intersect_within",
        "join_overlap_intersect_within_directed",
        "join_overlap_left",
        "join_overlap_left_directed",
        "join_overlap_left_within",
        "join_overlap_left_within_directed"
      ]
    },
    {
      "page": "ranges-overlaps-self",
      "title": "Find overlaps within a Ranges object",
      "topics": [
        "join_overlap_self",
        "join_overlap_self_directed",
        "join_overlap_self_within",
        "join_overlap_self_within_directed"
      ]
    },
    {
      "page": "ranges-precede",
      "title": "Find preceding Ranges",
      "topics": [
        "join_precede",
        "join_precede_downstream",
        "join_precede_right"
      ]
    },
    {
      "page": "mutate-ranges",
      "title": "Modify a Ranges object",
      "topics": [
        "mutate.Ranges"
      ]
    },
    {
      "page": "n",
      "title": "Compute the number of ranges in each group.",
      "topics": [
        "n"
      ]
    },
    {
      "page": "n_distinct",
      "title": "Compute the number of distinct unique values in a vector or List",
      "topics": [
        "n_distinct"
      ]
    },
    {
      "page": "overscope_ranges",
      "title": "Create an overscoped environment from a Ranges object",
      "topics": [
        "overscope_ranges"
      ]
    },
    {
      "page": "ranges-pairs",
      "title": "Pair together two ranges objects",
      "topics": [
        "pair_follow",
        "pair_nearest",
        "pair_overlaps",
        "pair_precede"
      ]
    },
    {
      "page": "pull-ranges",
      "title": "Extract a single column from a Ranges object as a vector",
      "topics": [
        "pull-ranges",
        "pull.Ranges"
      ]
    },
    {
      "page": "ranges-info",
      "title": "Construct annotation information",
      "topics": [
        "genome_info",
        "get_genome_info",
        "ranges-info",
        "set_genome_info"
      ]
    },
    {
      "page": "io-bam-read",
      "title": "Read a BAM file",
      "topics": [
        "read_bam"
      ]
    },
    {
      "page": "io-bed-read",
      "title": "Read a BED or BEDGraph file",
      "topics": [
        "read_bed",
        "read_bed_graph",
        "read_narrowpeaks"
      ]
    },
    {
      "page": "io-bigwig-read",
      "title": "Read a BigWig file",
      "topics": [
        "read_bigwig"
      ]
    },
    {
      "page": "io-gff-read",
      "title": "Read a GFF/GTF/GVT file",
      "topics": [
        "read_gff",
        "read_gff1",
        "read_gff2",
        "read_gff3"
      ]
    },
    {
      "page": "io-wig-read",
      "title": "Read a WIG file",
      "topics": [
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      ]
    },
    {
      "page": "ranges-reduce",
      "title": "Reduce then aggregate a Ranges object",
      "topics": [
        "reduce_ranges",
        "reduce_ranges_directed"
      ]
    },
    {
      "page": "ranges-names",
      "title": "Tools for working with named Ranges",
      "topics": [
        "id_to_column",
        "names_to_column",
        "remove_names"
      ]
    },
    {
      "page": "ranges-select",
      "title": "Select metadata columns of the Ranges object by name or position",
      "topics": [
        "select.Ranges"
      ]
    },
    {
      "page": "ranges-setters",
      "title": "Functional setters for Ranges objects",
      "topics": [
        "set_end",
        "set_seqnames",
        "set_start",
        "set_strand",
        "set_width"
      ]
    },
    {
      "page": "ranges-shift",
      "title": "Shift all coordinates in a genomic interval left or right, upstream or downstream",
      "topics": [
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        "shift_left",
        "shift_right",
        "shift_upstream"
      ]
    },
    {
      "page": "slice-ranges",
      "title": "Choose ranges by their position",
      "topics": [
        "slice.GroupedGenomicRanges",
        "slice.GroupedIntegerRanges",
        "slice.Ranges",
        "slice_head.GroupedGenomicRanges",
        "slice_head.GroupedIntegerRanges",
        "slice_head.Ranges",
        "slice_max.GroupedGenomicRanges",
        "slice_max.GroupedIntegerRanges",
        "slice_max.Ranges",
        "slice_min.GroupedGenomicRanges",
        "slice_min.GroupedIntegerRanges",
        "slice_min.Ranges",
        "slice_sample.GroupedGenomicRanges",
        "slice_sample.GroupedIntegerRanges",
        "slice_sample.Ranges",
        "slice_tail.GroupedGenomicRanges",
        "slice_tail.GroupedIntegerRanges",
        "slice_tail.Ranges"
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    },
    {
      "page": "stretch",
      "title": "Stretch a genomic interval",
      "topics": [
        "stretch"
      ]
    },
    {
      "page": "ranges-summarise",
      "title": "Reduce multiple values in a Ranges down to a single value",
      "topics": [
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    },
    {
      "page": "ranges-tile",
      "title": "Slide or tile over a Ranges object",
      "topics": [
        "slide_ranges",
        "tile_ranges"
      ]
    },
    {
      "page": "io-bed-write",
      "title": "Write a BED or BEDGraph file",
      "topics": [
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        "write_bed_graph",
        "write_narrowpeaks"
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    },
    {
      "page": "io-bigwig-write",
      "title": "Write a BigWig file",
      "topics": [
        "write_bigwig"
      ]
    },
    {
      "page": "io-gff-write",
      "title": "Write a GFF(123) file",
      "topics": [
        "write_gff",
        "write_gff1",
        "write_gff2",
        "write_gff3"
      ]
    },
    {
      "page": "io-wig-write",
      "title": "Write a WIG file",
      "topics": [
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  "_vignettes": [
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      "source": "more-examples.Rmd",
      "filename": "more-examples.html",
      "title": "Additional examples of plyranges",
      "author": "Stuart Lee",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Quick overview",
        "About Ranges",
        "Example: finding GWAS hits that overlap known exons",
        "Session information"
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      "created": "2026-03-15 18:52:39",
      "modified": "2026-03-15 18:52:39",
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      "filename": "an-introduction.html",
      "title": "Getting started with the plyranges package",
      "author": "Stuart Lee",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Ranges revisited",
        "Constructing Ranges",
        "Arithmetic on Ranges",
        "Grouping Ranges",
        "Restricting Ranges",
        "Summarising Ranges",
        "Joins, or another way at looking at overlaps between Ranges",
        "Finding your neighbours",
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        "Grouping by overlaps",
        "Data Import/Output",
        "Learning more",
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      "created": "2018-01-10 10:38:38",
      "modified": "2026-03-15 18:52:39",
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