{
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  "Package": "plyinteractions",
  "Title": "Extending tidy verbs to genomic interactions",
  "Description": "Operate on `GInteractions` objects as tabular data using\n`dplyr`-like verbs. The functions and methods in\n`plyinteractions` provide a grammatical approach to manipulate\n`GInteractions`, to facilitate their integration in genomic\nanalysis workflows.",
  "Version": "1.11.1",
  "Date": "2026-01-07",
  "Authors@R": "c(person(\"Jacques\", \"Serizay\", , \"jacquesserizay@gmail.com\",\nrole = c(\"aut\", \"cre\")\n))",
  "License": "Artistic-2.0",
  "URL": "https://github.com/js2264/plyinteractions",
  "BugReports": "https://github.com/js2264/plyinteractions/issues",
  "biocViews": "Software, Infrastructure",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-03 21:19:59 UTC",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "Author": "Jacques Serizay [aut, cre]",
  "Maintainer": "Jacques Serizay <jacquesserizay@gmail.com>",
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    "end2",
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    "seqnames2",
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    "shift_right",
    "shift_upstream",
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    "start1",
    "start2",
    "strand1",
    "strand2",
    "unpin",
    "width1",
    "width2",
    "write_bedpe",
    "write_pairs"
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      "title": "Data files provided in the plyinteractions package",
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      "file": "ce10_ARCC.rda",
      "class": [
        "GInteractions"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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    {
      "name": "ce10_REs",
      "title": "Data files provided in the plyinteractions package",
      "object": "ce10_REs",
      "file": "ce10_REs.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "GM12878_HiCCUPS",
      "title": "Data files provided in the plyinteractions package",
      "object": "GM12878_HiCCUPS",
      "file": "GM12878_HiCCUPS.rda",
      "class": [
        "GInteractions"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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    {
      "page": "add-pairdist",
      "title": "Appends distance between interaction anchors",
      "topics": [
        "add_pairdist"
      ]
    },
    {
      "page": "ginteractions-getters",
      "title": "Enhanced GInteractions getters",
      "topics": [
        "$,GInteractions-method",
        "anchors1",
        "anchors1,GInteractions-method",
        "anchors2",
        "anchors2,GInteractions-method",
        "end1",
        "end1,GInteractions-method",
        "end2",
        "end2,GInteractions-method",
        "ginteractions-getters",
        "ranges1",
        "ranges1,GInteractions-method",
        "ranges2",
        "ranges2,GInteractions-method",
        "seqnames1",
        "seqnames1,GInteractions-method",
        "seqnames2",
        "seqnames2,GInteractions-method",
        "start1",
        "start1,GInteractions-method",
        "start2",
        "start2,GInteractions-method",
        "strand1",
        "strand1,GInteractions-method",
        "strand2",
        "strand2,GInteractions-method",
        "width1",
        "width1,GInteractions-method",
        "width2",
        "width2,GInteractions-method"
      ]
    },
    {
      "page": "ginteractions-annotate",
      "title": "Annotate both anchors of a GInteractions",
      "topics": [
        "annotate",
        "annotate,GInteractions,GRanges,character-method",
        "annotate_directed",
        "annotate_directed,GInteractions,GRanges,character-method",
        "ginteractions-annotate"
      ]
    },
    {
      "page": "ginteractions-construct",
      "title": "Construct a GInteractions object from a tibble, DataFrame or data.frame",
      "topics": [
        "as_ginteractions"
      ]
    },
    {
      "page": "ginteractions-as_tibble",
      "title": "Turn a GInteractions object into a tibble",
      "topics": [
        "as_tibble.GInteractions"
      ]
    },
    {
      "page": "dplyr-arrange",
      "title": "Arrange a GInteractions by a column",
      "topics": [
        "arrange.GInteractions",
        "dplyr-arrange"
      ]
    },
    {
      "page": "dplyr-count",
      "title": "Count or tally GInteractions per group",
      "topics": [
        "count.GInteractions",
        "count.GroupedGInteractions",
        "dplyr-count",
        "tally.GroupedGInteractions"
      ]
    },
    {
      "page": "dplyr-filter",
      "title": "Subset a GInteractions with tidyverse-like 'filter'",
      "topics": [
        "dplyr-filter",
        "filter.GInteractions"
      ]
    },
    {
      "page": "dplyr-group_by",
      "title": "Group GInteractions by columns",
      "topics": [
        "dplyr-group_by",
        "group_by.DelegatingGInteractions",
        "group_by.GInteractions",
        "ungroup.GroupedGInteractions"
      ]
    },
    {
      "page": "dplyr-mutate",
      "title": "Mutate columns from a GInteractions object",
      "topics": [
        "dplyr-mutate",
        "mutate.GInteractions",
        "mutate.GroupedGInteractions"
      ]
    },
    {
      "page": "dplyr-rename",
      "title": "Rename columns from a GInteractions with tidyverse-like 'rename'",
      "topics": [
        "dplyr-rename",
        "rename.GInteractions"
      ]
    },
    {
      "page": "dplyr-select",
      "title": "Select columns within GInteractions metadata columns",
      "topics": [
        "dplyr-select",
        "select.GInteractions"
      ]
    },
    {
      "page": "dplyr-slice",
      "title": "Slice a GInteractions rows by their index",
      "topics": [
        "dplyr-slice",
        "slice.GInteractions"
      ]
    },
    {
      "page": "dplyr-summarize",
      "title": "Summarize GInteractions per group",
      "topics": [
        "dplyr-summarise",
        "dplyr-summarize",
        "summarise.GroupedGInteractions",
        "summarize.GroupedGInteractions"
      ]
    },
    {
      "page": "ginteractions-anchor",
      "title": "Manage GInteractions anchors with plyranges",
      "topics": [
        "anchor.AnchoredPinnedGInteractions",
        "anchor_3p.AnchoredPinnedGInteractions",
        "anchor_3p.PinnedGInteractions",
        "anchor_5p.AnchoredPinnedGInteractions",
        "anchor_5p.PinnedGInteractions",
        "anchor_center.AnchoredPinnedGInteractions",
        "anchor_center.PinnedGInteractions",
        "anchor_end.AnchoredPinnedGInteractions",
        "anchor_end.PinnedGInteractions",
        "anchor_start.AnchoredPinnedGInteractions",
        "anchor_start.PinnedGInteractions",
        "ginteractions-anchor",
        "unanchor.AnchoredPinnedGInteractions"
      ]
    },
    {
      "page": "ginteractions-count-overlaps",
      "title": "Count overlaps between a query GInteractions and a GRanges",
      "topics": [
        "count_overlaps.GInteractions",
        "count_overlaps.PinnedGInteractions",
        "count_overlaps_directed.GInteractions",
        "count_overlaps_directed.PinnedGInteractions",
        "ginteractions-count-overlaps"
      ]
    },
    {
      "page": "ginteractions-export",
      "title": "Export GInteractions as 'bedpe' or 'pairs' files",
      "topics": [
        "ginteractions-export",
        "write_bedpe",
        "write_pairs"
      ]
    },
    {
      "page": "ginteractions-filter-overlaps",
      "title": "Filter GInteractions overlapping with a GRanges",
      "topics": [
        "filter_by_non_overlaps.GInteractions",
        "filter_by_non_overlaps.PinnedGInteractions",
        "filter_by_overlaps.GInteractions",
        "filter_by_overlaps.PinnedGInteractions",
        "ginteractions-filter-overlaps"
      ]
    },
    {
      "page": "ginteractions-find-overlaps",
      "title": "Find overlaps between a query GInteractions and a GRanges",
      "topics": [
        "find_overlaps.GInteractions",
        "find_overlaps.PinnedGInteractions",
        "find_overlaps_directed.GInteractions",
        "find_overlaps_directed.PinnedGInteractions",
        "ginteractions-find-overlaps"
      ]
    },
    {
      "page": "ginteractions-join-overlap-left",
      "title": "Join overlaps between a query GInteractions and a GRanges",
      "topics": [
        "ginteractions-join-overlap-left",
        "join_overlap_left.GInteractions",
        "join_overlap_left.PinnedGInteractions",
        "join_overlap_left_directed.GInteractions",
        "join_overlap_left_directed.PinnedGInteractions"
      ]
    },
    {
      "page": "group-group_data",
      "title": "GInteractions grouping metadata",
      "topics": [
        "group-group_data",
        "groups.GroupedGInteractions",
        "group_data.GroupedGInteractions",
        "group_indices.GroupedGInteractions",
        "group_keys.GroupedGInteractions",
        "group_size.GroupedGInteractions",
        "group_vars.GInteractions",
        "group_vars.GroupedGInteractions",
        "n_groups.GroupedGInteractions"
      ]
    },
    {
      "page": "pair-granges",
      "title": "Pairwise combination of a GRanges object",
      "topics": [
        "pair_granges"
      ]
    },
    {
      "page": "ginteractions-pin",
      "title": "Pin GInteractions by anchors set (anchors1 or anchors2).",
      "topics": [
        "ginteractions-pin",
        "pin",
        "pin,AnchoredPinnedGInteractions,character-method",
        "pin,AnchoredPinnedGInteractions,numeric-method",
        "pin,GInteractions,character-method",
        "pin,GInteractions,numeric-method",
        "pin,GroupedGInteractions,character-method",
        "pin,GroupedGInteractions,numeric-method",
        "pin,PinnedGInteractions,character-method",
        "pin,PinnedGInteractions,missing-method",
        "pin,PinnedGInteractions,numeric-method",
        "pinned_anchors",
        "pinned_anchors,AnchoredPinnedGInteractions-method",
        "pinned_anchors,PinnedGInteractions-method",
        "pin_anchors1",
        "pin_anchors2",
        "pin_by",
        "pin_first",
        "pin_second",
        "unpin",
        "unpin,AnchoredPinnedGInteractions-method",
        "unpin,GInteractions-method",
        "unpin,PinnedGInteractions-method"
      ]
    },
    {
      "page": "plyinteractions-data",
      "title": "Data files provided in the plyinteractions package",
      "topics": [
        "ce10_ARCC",
        "ce10_REs",
        "GM12878_HiCCUPS",
        "plyinteractions-data"
      ]
    },
    {
      "page": "plyinteractions-flank",
      "title": "Generate flanking regions from pinned anchors of a GInteractions object",
      "topics": [
        "flank_downstream",
        "flank_downstream.PinnedGInteractions",
        "flank_downstream.Ranges",
        "flank_left",
        "flank_left.PinnedGInteractions",
        "flank_left.Ranges",
        "flank_right",
        "flank_right.PinnedGInteractions",
        "flank_right.Ranges",
        "flank_upstream",
        "flank_upstream.PinnedGInteractions",
        "flank_upstream.Ranges",
        "plyinteractions-flank"
      ]
    },
    {
      "page": "plyinteractions-shift",
      "title": "Shift pinned anchors of a GInteractions object with plyinteractions",
      "topics": [
        "plyinteractions-shift",
        "shift_downstream",
        "shift_downstream.PinnedGInteractions",
        "shift_downstream.Ranges",
        "shift_left",
        "shift_left.PinnedGInteractions",
        "shift_left.Ranges",
        "shift_right",
        "shift_right.PinnedGInteractions",
        "shift_right.Ranges",
        "shift_upstream",
        "shift_upstream.PinnedGInteractions",
        "shift_upstream.Ranges"
      ]
    },
    {
      "page": "plyranges-stretch",
      "title": "Stretch pinned anchors of a GInteractions object with plyranges",
      "topics": [
        "plyranges-stretch",
        "stretch.AnchoredPinnedGInteractions",
        "stretch.PinnedGInteractions"
      ]
    },
    {
      "page": "replace_anchors",
      "title": "Replace anchors of a GInteractions",
      "topics": [
        "replace_anchors",
        "replace_anchors,AnchoredPinnedGInteractions,missing,GRanges-method",
        "replace_anchors,AnchoredPinnedGInteractions,numeric,GRanges-method",
        "replace_anchors,GInteractions,character,GenomicRanges-method",
        "replace_anchors,GInteractions,numeric,GenomicRanges-method",
        "replace_anchors,PinnedGInteractions,missing,GenomicRanges-method"
      ]
    },
    {
      "page": "show-GInteractions",
      "title": "show method for 'GInteractions' objects",
      "topics": [
        "show,AnchoredPinnedGInteractions-method",
        "show,GInteractions-method",
        "show,GroupedGInteractions-method",
        "show,PinnedGInteractions-method",
        "show-GInteractions"
      ]
    }
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