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  "Date": "2025-07-15",
  "Title": "Base Classes for Storing Genomic Interaction Data",
  "Authors@R": "c(person(\"Aaron\", \"Lun\", role = c(\"aut\", \"cre\"), email = \"infinite.monkeys.with.keyboards@gmail.com\"),\nperson(\"Malcolm\", \"Perry\", role = \"aut\", email = \"mgperry32@gmail.com\"),\nperson(\"Elizabeth\", \"Ing-Simmons\", role = \"aut\"))",
  "biocViews": "Infrastructure, DataRepresentation, Software, HiC",
  "Description": "Provides the GInteractions, InteractionSet and\nContactMatrix objects and associated methods for storing and\nmanipulating genomic interaction data from Hi-C and ChIA-PET\nexperiments.",
  "License": "GPL-3",
  "NeedsCompilation": "yes",
  "SystemRequirements": "C++11",
  "VignetteBuilder": "knitr",
  "Collate": "AllGenerics.R AllClasses.R ContactMatrix-methods.R\nGInteractions-methods.R InteractionSet-methods.R\nGRanges-methods.R getset.R swapAnchors.R pairs.R conversion.R\nlinearize.R boundingBox.R distances.R overlaps.R linkOverlaps.R\nmatching.R updateObject.R",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:23 UTC",
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  "Author": "Aaron Lun [aut, cre],\nMalcolm Perry [aut],\nElizabeth Ing-Simmons [aut]",
  "Maintainer": "Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
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    },
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_exports": [
    "anchorIds",
    "anchorIds<-",
    "anchors",
    "appendRegions<-",
    "as.matrix<-",
    "boundingBox",
    "ContactMatrix",
    "countOverlaps",
    "deflate",
    "findOverlaps",
    "GInteractions",
    "inflate",
    "interactions",
    "interactions<-",
    "InteractionSet",
    "intrachr",
    "linearize",
    "linkOverlaps",
    "makeGInteractionsFromGRangesPairs",
    "overlapsAny",
    "pairdist",
    "pairs",
    "reduceRegions",
    "regions",
    "regions<-",
    "replaceRegions<-",
    "seqinfo",
    "seqinfo<-",
    "swapAnchors",
    "updateObject"
  ],
  "_help": [
    {
      "page": "boundingBox",
      "title": "Get the bounding box",
      "topics": [
        "boundingBox",
        "boundingBox,GInteractions-method",
        "boundingBox,InteractionSet-method"
      ]
    },
    {
      "page": "ContactMatrix-accessors",
      "title": "ContactMatrix accessors",
      "topics": [
        "anchorIds,ContactMatrix-method",
        "anchorIds<-,ContactMatrix-method",
        "anchors,ContactMatrix-method",
        "anchors<-,ContactMatrix-method",
        "appendRegions<-,ContactMatrix-method",
        "as.matrix,ContactMatrix-method",
        "as.matrix<-",
        "as.matrix<-,ContactMatrix-method",
        "ContactMatrix-access",
        "dim,ContactMatrix-method",
        "dimnames,ContactMatrix-method",
        "dimnames<-,ContactMatrix,ANY-method",
        "dimnames<-,ContactMatrix-method",
        "length,ContactMatrix-method",
        "reduceRegions,ContactMatrix-method",
        "regions,ContactMatrix-method",
        "regions<-,ContactMatrix-method",
        "replaceRegions<-,ContactMatrix-method",
        "seqinfo,ContactMatrix-method",
        "seqinfo<-,ContactMatrix-method",
        "show,ContactMatrix-method",
        "t,ContactMatrix-method"
      ]
    },
    {
      "page": "ContactMatrix-class",
      "title": "ContactMatrix class and constructors",
      "topics": [
        "ContactMatrix",
        "ContactMatrix,ANY,GRanges,GRanges,GenomicRanges_OR_missing-method",
        "ContactMatrix,ANY,numeric,numeric,GRanges-method",
        "ContactMatrix,missing,missing,missing,GenomicRanges_OR_missing-method",
        "ContactMatrix-class"
      ]
    },
    {
      "page": "ContactMatrix-distances",
      "title": "Compute linear distances from ContactMatrix objects",
      "topics": [
        "ContactMatrix-dist",
        "intrachr,ContactMatrix-method",
        "pairdist,ContactMatrix-method"
      ]
    },
    {
      "page": "ContactMatrix-overlaps",
      "title": "Find overlaps between GRanges and a ContactMatrix",
      "topics": [
        "overlapsAny,ContactMatrix,GInteractions-method",
        "overlapsAny,ContactMatrix,InteractionSet-method",
        "overlapsAny,ContactMatrix,Vector-method"
      ]
    },
    {
      "page": "ContactMatrix-sorting",
      "title": "ContactMatrix sorting and ordering",
      "topics": [
        "ContactMatrix-sort",
        "duplicated,ContactMatrix-method",
        "order,ContactMatrix-method",
        "sort,ContactMatrix-method",
        "unique,ContactMatrix-method"
      ]
    },
    {
      "page": "ContactMatrix-subset",
      "title": "ContactMatrix subsetting and combining",
      "topics": [
        "cbind,ContactMatrix-method",
        "ContactMatrix-subset",
        "rbind,ContactMatrix-method",
        "subset,ContactMatrix-method",
        "[,ContactMatrix,ANY,ANY,ANY-method",
        "[,ContactMatrix,ANY,ANY-method",
        "[,ContactMatrix,ANY-method",
        "[<-,ContactMatrix,ANY,ANY,ContactMatrix-method"
      ]
    },
    {
      "page": "conversion",
      "title": "Convert between classes",
      "topics": [
        "deflate",
        "deflate,ContactMatrix-method",
        "inflate",
        "inflate,GInteractions-method",
        "inflate,InteractionSet-method"
      ]
    },
    {
      "page": "GInteractions-class",
      "title": "GInteractions class and constructors",
      "topics": [
        "GInteractions",
        "GInteractions,GRanges,GRanges,GenomicRanges_OR_missing-method",
        "GInteractions,missing,missing,GenomicRanges_OR_missing-method",
        "GInteractions,numeric,numeric,GRanges-method",
        "GInteractions-class",
        "ReverseStrictGInteractions-class",
        "StrictGInteractions-class"
      ]
    },
    {
      "page": "granges-methods",
      "title": "Equivalents of GRanges methods",
      "topics": [
        "flank,ContactMatrix-method",
        "flank,GInteractions-method",
        "flank,InteractionSet-method",
        "narrow,ContactMatrix-method",
        "narrow,GInteractions-method",
        "narrow,InteractionSet-method",
        "resize,ContactMatrix-method",
        "resize,GInteractions-method",
        "resize,InteractionSet-method",
        "shift,ContactMatrix-method",
        "shift,GInteractions-method",
        "shift,InteractionSet-method",
        "trim,ContactMatrix-method",
        "trim,GInteractions-method",
        "trim,InteractionSet-method",
        "width,ContactMatrix-method",
        "width,GInteractions-method",
        "width,InteractionSet-method"
      ]
    },
    {
      "page": "interaction-accessors",
      "title": "Interaction accessors",
      "topics": [
        "$,GInteractions-method",
        "$<-,GInteractions-method",
        "anchorIds",
        "anchorIds,GInteractions-method",
        "anchorIds,InteractionSet-method",
        "anchorIds<-",
        "anchorIds<-,GInteractions-method",
        "anchorIds<-,InteractionSet-method",
        "anchorIds<-,ReverseStrictGInteractions-method",
        "anchorIds<-,StrictGInteractions-method",
        "anchors",
        "anchors,GInteractions-method",
        "anchors,InteractionSet-method",
        "anchors<-",
        "anchors<-,GInteractions-method",
        "anchors<-,InteractionSet-method",
        "anchors<-,ReverseStrictGInteractions-method",
        "anchors<-,StrictGInteractions-method",
        "appendRegions<-",
        "appendRegions<-,GInteractions-method",
        "appendRegions<-,InteractionSet-method",
        "as.data.frame,GInteractions-method",
        "first",
        "first,GInteractions-method",
        "first,InteractionSet-method",
        "interaction-access",
        "interactions",
        "interactions,InteractionSet-method",
        "interactions<-",
        "interactions<-,InteractionSet-method",
        "length,GInteractions-method",
        "mcols,InteractionSet-method",
        "mcols<-,InteractionSet-method",
        "names,GInteractions-method",
        "names,InteractionSet-method",
        "names<-,GInteractions-method",
        "names<-,InteractionSet-method",
        "reduceRegions",
        "reduceRegions,GInteractions-method",
        "reduceRegions,InteractionSet-method",
        "regions",
        "regions,GInteractions-method",
        "regions,InteractionSet-method",
        "regions<-",
        "regions<-,GInteractions-method",
        "regions<-,InteractionSet-method",
        "replaceRegions<-",
        "replaceRegions<-,GInteractions-method",
        "replaceRegions<-,InteractionSet-method",
        "second",
        "second,GInteractions-method",
        "second,InteractionSet-method",
        "seqinfo,GInteractions-method",
        "seqinfo,InteractionSet-method",
        "seqinfo<-,GInteractions-method",
        "seqinfo<-,InteractionSet-method",
        "show,GInteractions-method",
        "show,InteractionSet-method"
      ]
    },
    {
      "page": "interaction-bind",
      "title": "Interaction combining",
      "topics": [
        "c,GInteractions-method",
        "cbind,InteractionSet-method",
        "interaction-bind",
        "rbind,InteractionSet-method"
      ]
    },
    {
      "page": "interaction-compare",
      "title": "Interaction comparisons",
      "topics": [
        "duplicated,GInteractions-method",
        "duplicated,InteractionSet-method",
        "interaction-compare",
        "match,GInteractions,GInteractions-method",
        "match,GInteractions,InteractionSet-method",
        "match,InteractionSet,GInteractions-method",
        "match,InteractionSet,InteractionSet-method",
        "order,GInteractions-method",
        "order,InteractionSet-method",
        "pcompare,GInteractions,GInteractions-method",
        "sort,GInteractions-method",
        "sort,InteractionSet-method",
        "swapAnchors",
        "swapAnchors,GInteractions-method",
        "swapAnchors,InteractionSet-method",
        "unique,GInteractions-method",
        "unique,InteractionSet-method"
      ]
    },
    {
      "page": "distances",
      "title": "Get the linear distance for each interaction",
      "topics": [
        "intrachr",
        "intrachr,GInteractions-method",
        "intrachr,InteractionSet-method",
        "pairdist",
        "pairdist,GInteractions-method",
        "pairdist,InteractionSet-method"
      ]
    },
    {
      "page": "overlaps",
      "title": "Find overlaps between interactions in one or two dimensions",
      "topics": [
        "countOverlaps",
        "countOverlaps,GInteractions,GInteractions-method",
        "countOverlaps,GInteractions,InteractionSet-method",
        "countOverlaps,GInteractions,missing-method",
        "countOverlaps,GInteractions,Vector-method",
        "countOverlaps,InteractionSet,GInteractions-method",
        "countOverlaps,InteractionSet,InteractionSet-method",
        "countOverlaps,InteractionSet,missing-method",
        "countOverlaps,InteractionSet,Vector-method",
        "countOverlaps,Vector,GInteractions-method",
        "countOverlaps,Vector,InteractionSet-method",
        "findOverlaps",
        "findOverlaps,GInteractions,GInteractions-method",
        "findOverlaps,GInteractions,InteractionSet-method",
        "findOverlaps,GInteractions,missing-method",
        "findOverlaps,GInteractions,Vector-method",
        "findOverlaps,InteractionSet,GInteractions-method",
        "findOverlaps,InteractionSet,InteractionSet-method",
        "findOverlaps,InteractionSet,missing-method",
        "findOverlaps,InteractionSet,Vector-method",
        "findOverlaps,Vector,GInteractions-method",
        "findOverlaps,Vector,InteractionSet-method",
        "Interaction-overlaps",
        "overlapsAny",
        "overlapsAny,GInteractions,GInteractions-method",
        "overlapsAny,GInteractions,InteractionSet-method",
        "overlapsAny,GInteractions,missing-method",
        "overlapsAny,GInteractions,Vector-method",
        "overlapsAny,InteractionSet,GInteractions-method",
        "overlapsAny,InteractionSet,InteractionSet-method",
        "overlapsAny,InteractionSet,missing-method",
        "overlapsAny,InteractionSet,Vector-method",
        "overlapsAny,Vector,GInteractions-method",
        "overlapsAny,Vector,InteractionSet-method",
        "subsetByOverlaps",
        "subsetByOverlaps,GInteractions,GInteractions-method",
        "subsetByOverlaps,GInteractions,InteractionSet-method",
        "subsetByOverlaps,GInteractions,Vector-method",
        "subsetByOverlaps,InteractionSet,GInteractions-method",
        "subsetByOverlaps,InteractionSet,InteractionSet-method",
        "subsetByOverlaps,InteractionSet,Vector-method",
        "subsetByOverlaps,Vector,GInteractions-method",
        "subsetByOverlaps,Vector,InteractionSet-method"
      ]
    },
    {
      "page": "interaction-subset",
      "title": "Interaction subsetting and combining",
      "topics": [
        "interaction-subset",
        "subset,InteractionSet-method",
        "[,InteractionSet,ANY,ANY,ANY-method",
        "[,InteractionSet,ANY,ANY-method",
        "[,InteractionSet,ANY-method",
        "[<-,GInteractions,ANY,GInteractions-method",
        "[<-,InteractionSet,ANY,ANY,InteractionSet-method"
      ]
    },
    {
      "page": "InteractionSet-class",
      "title": "InteractionSet class and constructors",
      "topics": [
        "InteractionSet",
        "InteractionSet,ANY,GInteractions-method",
        "InteractionSet,missing,missing-method",
        "InteractionSet-class"
      ]
    },
    {
      "page": "linearize",
      "title": "Linearize 2D interactions into 1D ranges",
      "topics": [
        "linearize",
        "linearize,GInteractions,GRanges-method",
        "linearize,GInteractions,numeric-method",
        "linearize,InteractionSet,GRanges-method",
        "linearize,InteractionSet,numeric-method"
      ]
    },
    {
      "page": "linkOverlaps",
      "title": "Link overlapping regions",
      "topics": [
        "linkOverlaps",
        "linkOverlaps,GInteractions,Hits,Hits-method",
        "linkOverlaps,GInteractions,Hits,missing-method",
        "linkOverlaps,GInteractions,Vector,missing-method",
        "linkOverlaps,GInteractions,Vector,Vector-method",
        "linkOverlaps,InteractionSet,Hits,Hits-method",
        "linkOverlaps,InteractionSet,Hits,missing-method",
        "linkOverlaps,InteractionSet,Vector,missing-method",
        "linkOverlaps,InteractionSet,Vector,Vector-method"
      ]
    },
    {
      "page": "pairs",
      "title": "Extract paired ranges",
      "topics": [
        "makeGInteractionsFromGRangesPairs",
        "pairs",
        "pairs,GInteractions-method",
        "pairs,InteractionSet-method"
      ]
    },
    {
      "page": "updateObject",
      "title": "Update a GInteractions object",
      "topics": [
        "updateObject",
        "updateObject,GInteractions-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/InteractionSet/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "DelayedArray",
    "generics",
    "GenomicRanges",
    "IRanges",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "Rcpp",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SparseArray",
    "SummarizedExperiment",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "interactions.Rmd",
      "filename": "interactions.html",
      "title": "Classes for genomic interaction data",
      "author": "Aaron Lun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Description of the GInteractions class",
        "Construction",
        "Getters",
        "Setters",
        "Subsetting and combining",
        "Sorting, duplication and matching",
        "Distance calculations",
        "Overlap methods",
        "Linking sets of regions",
        "Finding the bounding box",
        "Enforcing anchor ordering in StrictGInteractions",
        "Description of the InteractionSet class",
        "Other methods",
        "Description of the ContactMatrix class",
        "Sorting and duplication",
        "Distance calculation",
        "Converting between classes",
        "Inflating a GInteractions into a ContactMatrix",
        "Deflating a ContactMatrix into an InteractionSet",
        "Linearizing an InteractionSet into a RangedSummarizedExperiment",
        "Summary"
      ],
      "created": "2016-04-06 16:10:37",
      "modified": "2021-04-16 07:34:39",
      "commits": 4
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