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  "Package": "GenomicInteractions",
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  "Title": "Utilities for handling genomic interaction data",
  "URL": "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/",
  "Version": "1.47.0",
  "Date": "2025-07-22",
  "Author": "Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., Lenhard,\nB.",
  "Maintainer": "Liz Ing-Simmons <liz.ingsimmons@gmail.com>",
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  "Description": "Utilities for handling genomic interaction data such as\nChIA-PET or Hi-C, annotating genomic features with interaction\ninformation, and producing plots and summary statistics.",
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  "Date/Publication": "2026-04-28 12:39:48 UTC",
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    "anchorTwo",
    "annotateInteractions",
    "annotateRegions",
    "annotationFeatures",
    "asBED",
    "availableDisplayPars",
    "calculateDistances",
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    "countsBetweenAnchors",
    "description",
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    "end",
    "export.bed12",
    "export.bedpe",
    "export.chiasig",
    "export.igraph",
    "GenomicInteractions",
    "get_binom_ligation_threshold",
    "get_self_ligation_threshold",
    "interactionCounts",
    "interactionCounts<-",
    "InteractionTrack",
    "is.cis",
    "is.dd",
    "is.dt",
    "is.pd",
    "is.pp",
    "is.pt",
    "is.trans",
    "is.tt",
    "isInteractionType",
    "makeGenomicInteractionsFromFile",
    "name",
    "name<-",
    "plotAvgViewpoint",
    "plotCisTrans",
    "plotCounts",
    "plotDists",
    "plotInteractionAnnotations",
    "plotSummaryStats",
    "plotViewpoint",
    "removeDups",
    "resetAnnotations",
    "start",
    "subset",
    "subsetByFeatures",
    "summariseByFeaturePairs",
    "summariseByFeatures",
    "updateObject",
    "viewPoint"
  ],
  "_datasets": [
    {
      "name": "hg19.refseq.transcripts",
      "title": "Human Refseq transcripts from chr 17-18",
      "object": "hg19.refseq.transcripts",
      "file": "hg19.refseq.transcripts.rda",
      "class": [
        "CompressedGRangesList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hic_example_data",
      "title": "Example HiC dataset",
      "object": "hic_example_data",
      "file": "hic_example_data.rda",
      "class": [
        "GenomicInteractions"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mm9_refseq_promoters",
      "title": "Mouse Refseq promoters from chr 14-15",
      "object": "mm9_refseq_promoters",
      "file": "mm9_refseq_promoters.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "thymus_enh",
      "title": "Putative enhancers from mouse thymus data",
      "object": "thymus_enhancers",
      "file": "thymus_enhancers.rda",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "GenomicInteractions-package",
      "title": "GenomicInteractions",
      "topics": [
        "GenomicInteractions-package"
      ]
    },
    {
      "page": "dot-importHicLib",
      "title": "Function to read in processed Hi-C interaction data generated by hiclib",
      "topics": [
        ".importHicLib"
      ]
    },
    {
      "page": "dot-importHomer",
      "title": "Function to read in processed Hi-C interaction data generated by HOMER",
      "topics": [
        ".importHomer"
      ]
    },
    {
      "page": "dot-processChiapetName",
      "title": "Function to process names relating to interactions stored in bed12 formats.",
      "topics": [
        ".processChiapetName"
      ]
    },
    {
      "page": "dot-readBam",
      "title": "Function to read in interaction-data stored in a BAM file",
      "topics": [
        ".readBam"
      ]
    },
    {
      "page": "dot-readTwoBams",
      "title": "Function to read in interaction-data stored in a pair of BAM files",
      "topics": [
        ".readTwoBams"
      ]
    },
    {
      "page": "dot-validateInput",
      "title": "Function to validate tabular input",
      "topics": [
        ".validateInput"
      ]
    },
    {
      "page": "annotateInteractions",
      "title": "Annotate the interactions in a GInteractions object",
      "topics": [
        "annotateInteractions",
        "annotateInteractions,GInteractions,list-method"
      ]
    },
    {
      "page": "annotateRegions",
      "title": "Annotate regions",
      "topics": [
        "annotateRegions",
        "annotateRegions,GInteractions,character,vector-method"
      ]
    },
    {
      "page": "asBED-GInteractions-method",
      "title": "Coerce to BED structure",
      "topics": [
        "asBED,GInteractions-method"
      ]
    },
    {
      "page": "availableDisplayPars",
      "title": "The default display parameters for a track object class can be queries using the availableDisplayPars function.",
      "topics": [
        "availableDisplayPars"
      ]
    },
    {
      "page": "calculateDistances",
      "title": "Calculate interaction distances",
      "topics": [
        "calculateDistances",
        "calculateDistances,GInteractions-method"
      ]
    },
    {
      "page": "categoriseInteractions",
      "title": "Get the numbers of interaction types existing in your data",
      "topics": [
        "categoriseInteractions"
      ]
    },
    {
      "page": "countsBetweenAnchors-methods",
      "title": "Summarise interactions between defined anchors",
      "topics": [
        "countsBetweenAnchors",
        "countsBetweenAnchors,GInteractions,GRanges-method"
      ]
    },
    {
      "page": "export.bed12",
      "title": "Export interactions in BED12 format.",
      "topics": [
        "export.bed12",
        "export.bed12,GInteractions-method"
      ]
    },
    {
      "page": "export.bedpe",
      "title": "Export interactions in BED Paired-End format.",
      "topics": [
        "export.bedpe",
        "export.bedpe,GInteractions-method"
      ]
    },
    {
      "page": "export.chiasig",
      "title": "Export interactions in a BEDPE-like format for use with ChiaSig",
      "topics": [
        "export.chiasig",
        "export.chiasig,GInteractions-method"
      ]
    },
    {
      "page": "export.igraph",
      "title": "Export interactions to an igraph object.",
      "topics": [
        "export.igraph",
        "export.igraph,GInteractions-method"
      ]
    },
    {
      "page": "GenomicInteractions",
      "title": "Function to create a GenomicInteractions object",
      "topics": [
        "GenomicInteractions",
        "GenomicInteractions,ANY,ANY,ANY-method",
        "GenomicInteractions,GInteractions,ANY,ANY-method",
        "GenomicInteractions,GInteractions,numeric,ANY-method",
        "GenomicInteractions,GRanges,GRanges,GenomicRanges_OR_missing-method",
        "GenomicInteractions,GRanges,GRanges,numeric-method",
        "GenomicInteractions,missing,missing,GenomicRanges_OR_missing-method",
        "GenomicInteractions,numeric,numeric,GRanges-method"
      ]
    },
    {
      "page": "GenomicInteractions-class",
      "title": "A S4 class to represent interactions between genomic regions.",
      "topics": [
        "GenomicInteractions-class"
      ]
    },
    {
      "page": "get_binom_ligation_threshold",
      "title": "get self ligation threshold with binomial test",
      "topics": [
        "get_binom_ligation_threshold"
      ]
    },
    {
      "page": "get_self_ligation_threshold",
      "title": "Get self ligation threshold with SD method from Heidari et al",
      "topics": [
        "get_self_ligation_threshold"
      ]
    },
    {
      "page": "getters",
      "title": "Functions to access data held in a GenomicInteractions object.",
      "topics": [
        "anchorOne",
        "anchorOne,GInteractions-method",
        "anchorTwo",
        "anchorTwo,GInteractions-method",
        "annotationFeatures",
        "annotationFeatures,GInteractions-method",
        "description,GInteractions-method",
        "getters",
        "interactionCounts",
        "interactionCounts,GInteractions-method",
        "name",
        "name,GInteractions-method"
      ]
    },
    {
      "page": "hg19.refseq.transcripts",
      "title": "Human Refseq transcripts from chr 17-18",
      "topics": [
        "hg19.refseq.transcripts"
      ]
    },
    {
      "page": "hic_example_data",
      "title": "Example HiC dataset",
      "topics": [
        "hic_example_data"
      ]
    },
    {
      "page": "InteractionTrack",
      "title": "Constructor to create an InteractionTrack object",
      "topics": [
        "InteractionTrack"
      ]
    },
    {
      "page": "InteractionTrack-class",
      "title": "A class to hold chromatin interaction data for a specific genomic region",
      "topics": [
        "chromosome,InteractionTrack-method",
        "end,InteractionTrack-method",
        "InteractionTrack-class",
        "start,InteractionTrack-method",
        "subset,InteractionTrack-method"
      ]
    },
    {
      "page": "InteractionHelpers",
      "title": "Interaction Type Helpers",
      "topics": [
        "InteractionHelpers",
        "is.cis",
        "is.cis,GInteractions-method",
        "is.dd",
        "is.dd,GInteractions-method",
        "is.dt",
        "is.dt,GInteractions-method",
        "is.pd",
        "is.pd,GInteractions-method",
        "is.pp",
        "is.pp,GInteractions-method",
        "is.pt",
        "is.pt,GInteractions-method",
        "is.trans",
        "is.trans,GInteractions-method",
        "is.tt",
        "is.tt,GInteractions-method",
        "isInteractionType",
        "isInteractionType,GInteractions-method"
      ]
    },
    {
      "page": "makeGenomicInteractionsFromFile",
      "title": "Function to create GenomicInteraction objects from a file",
      "topics": [
        "makeGenomicInteractionsFromFile"
      ]
    },
    {
      "page": "mm9_refseq_promoters",
      "title": "Mouse Refseq promoters from chr 14-15",
      "topics": [
        "mm9_refseq_promoters"
      ]
    },
    {
      "page": "plotAvgViewpoint",
      "title": "Plot coverage around a set of virtual 4C viewpoints",
      "topics": [
        "plotAvgViewpoint"
      ]
    },
    {
      "page": "plotCisTrans",
      "title": "Plots the percentages of cis and trans interactions for a GInteractions object as a donut plot.",
      "topics": [
        "plotCisTrans"
      ]
    },
    {
      "page": "plotCounts",
      "title": "Plot a bar chart of the number of interactions supported by different numbers of reads in your data.",
      "topics": [
        "plotCounts"
      ]
    },
    {
      "page": "plotDists",
      "title": "Plots a histogram of interaction distances for a GInteractions Object",
      "topics": [
        "plotDists"
      ]
    },
    {
      "page": "plotInteractionAnnotations",
      "title": "Plot a donut plot of interaction types for an annotated GInteractions object",
      "topics": [
        "plotInteractionAnnotations"
      ]
    },
    {
      "page": "plotSummaryStats",
      "title": "Plot summary statistics for a GInteractions object",
      "topics": [
        "plotSummaryStats"
      ]
    },
    {
      "page": "plotViewpoint",
      "title": "Plot coverage around a virtual 4C viewpoint",
      "topics": [
        "plotViewpoint"
      ]
    },
    {
      "page": "removeDups",
      "title": "Remove all but one occurences of a duplicated interaction",
      "topics": [
        "removeDups"
      ]
    },
    {
      "page": "resetAnnotations",
      "title": "Reset annotations made to a GInteractions object",
      "topics": [
        "resetAnnotations",
        "resetAnnotations,GInteractions-method"
      ]
    },
    {
      "page": "sameStrand",
      "title": "Tests whether anchors have the same strand.",
      "topics": [
        "sameStrand"
      ]
    },
    {
      "page": "setters",
      "title": "Functions to set data held in a GInteractions object.",
      "topics": [
        "description<-,GInteractions,ANY-method",
        "interactionCounts<-",
        "interactionCounts<-,GInteractions-method",
        "name<-",
        "name<-,GInteractions-method",
        "setters"
      ]
    },
    {
      "page": "GInteractions-subsetByFeatures-methods",
      "title": "Subset a GInteractions object by features",
      "topics": [
        "subsetByFeatures",
        "subsetByFeatures,GInteractions,character,character-method",
        "subsetByFeatures,GInteractions,GRanges,missing-method",
        "subsetByFeatures,GInteractions,GRangesList,missing-method"
      ]
    },
    {
      "page": "sum-GInteractions-method",
      "title": "Return the total number of interactions in a GInteractions GIObject",
      "topics": [
        "sum,GInteractions-method"
      ]
    },
    {
      "page": "summariseByFeaturePairs",
      "title": "Summarise the number of interactions between two sets of features.",
      "topics": [
        "summariseByFeaturePairs",
        "summariseByFeaturePairs,GInteractions-method"
      ]
    },
    {
      "page": "summariseByFeatures",
      "title": "Summary statistics of interactions for a given feature set",
      "topics": [
        "summariseByFeatures",
        "summariseByFeatures,GInteractions-method"
      ]
    },
    {
      "page": "thymus_enh",
      "title": "Putative enhancers from mouse thymus data",
      "topics": [
        "thymus_enh"
      ]
    },
    {
      "page": "updateObject-GenomicInteractions-method",
      "title": "updateObject method for GenomicInteractions 1.3.7 and earlier",
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