{
  "_id": "69b056331c98e56c7a62f571",
  "Package": "linkSet",
  "Title": "Base Classes for Storing Genomic Link Data",
  "Version": "1.1.0",
  "Authors@R": "c(person(\"Gilbert\", \"Han\", , \"GilbertHan1011@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0000-0293-2467\")))",
  "Description": "Provides a comprehensive framework for representing,\nanalyzing, and visualizing genomic interactions, particularly\nfocusing on gene-enhancer relationships. The package extends\nthe GenomicRanges infrastructure to handle paired genomic\nregions with specialized methods for chromatin interaction data\nfrom Hi-C, Promoter Capture Hi-C (PCHi-C), and single-cell\nATAC-seq experiments. Key features include conversion from\ncommon interaction formats, annotation of promoters and\nenhancers, distance-based analyses, interaction strength\nmetrics, statistical modeling using CHiCANE methodology, and\ntailored visualization tools. The package aims to standardize\nthe representation of genomic interaction data while providing\ndomain-specific functions not available in general genomic\ninteraction packages.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Collate": "class.R AllGenerics.R getset.R methods.R annotate.R distance.R\nformatConverter.R linkSet-package.R GRange_method.R\ntest_helper.R visualization.R count.R statical.R data.R",
  "biocViews": "Software, HiC, DataRepresentation, Sequencing, SingleCell,\nCoverage",
  "URL": "https://github.com/GilbertHan1011/linkSet,\nhttps://gilberthan1011.github.io/linkSet",
  "BugReports": "https://github.com/GilbertHan1011/linkSet/issues/new",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2025-10-29 15:37:12 UTC",
  "RemoteUrl": "https://github.com/bioc/linkSet",
  "RemoteRef": "HEAD",
  "RemoteSha": "bdadbdd362b9f200e14b5a7e144a7d13dd6a1881",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-03-10 08:59:11 UTC",
    "User": "root"
  },
  "Author": "Gilbert Han [aut, cre] (ORCID: <https://orcid.org/0009-0000-0293-2467>)",
  "Maintainer": "Gilbert Han <GilbertHan1011@gmail.com>",
  "MD5sum": "a3bf8849bde4bb989a3945e8787056cc",
  "_user": "bioc",
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  "_created": "2026-03-10T08:59:11.000Z",
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/22894436227",
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  "_upstream": "https://github.com/bioc/linkSet",
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    "id": "bdadbdd362b9f200e14b5a7e144a7d13dd6a1881",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_22 branch\n",
    "time": 1761752232
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  "_maintainer": {
    "name": "Gilbert Han",
    "email": "gilberthan1011@gmail.com",
    "login": "gilberthan1011",
    "uuid": 39906045
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  "_distro": "noble",
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  "_dependencies": [
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      "package": "GenomicRanges",
      "role": "Depends"
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    },
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      "role": "Imports"
    },
    {
      "package": "Organism.dplyr",
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  "_owner": "bioc",
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  "_updates": [
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    },
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    "hic",
    "datarepresentation",
    "sequencing",
    "singlecell",
    "coverage"
  ],
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  "_contributors": [
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  ],
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 118,
    "source": "https://www.bioconductor.org/packages/stats/bioc/linkSet"
  },
  "_devurl": "https://github.com/gilberthan1011/linkset",
  "_pkgdown": "https://gilberthan1011.github.io/linkSet",
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  "_rbuild": "4.5.2",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/gilberthan1011/linkset",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "anchor1",
    "anchor1<-",
    "anchor2",
    "anchor2<-",
    "anchorIds",
    "anchors",
    "annotateInter",
    "annotatePromoter",
    "as.GInteractions",
    "bait",
    "bait<-",
    "baitGInteractions",
    "clean_unused_regions",
    "cleanUnusedRegions",
    "Convert",
    "countInteractibility",
    "countInteractions",
    "crossGeneEnhancer",
    "diagnoseLinkSet",
    "exportInterBed",
    "exportWashU",
    "filterLinks",
    "flank",
    "flankRegions",
    "geom_linkset",
    "linkSet",
    "narrow",
    "narrowRegions",
    "oe",
    "oe<-",
    "orderLinks",
    "pairdist",
    "plot_genomic_ranges",
    "plotBaits",
    "plotGenomicRanges",
    "promoterRegions",
    "promoters",
    "readvalidPairs",
    "reduce",
    "reduceRegions",
    "regions",
    "regions<-",
    "regionsBait",
    "regionsBait<-",
    "resize",
    "resizeRegions",
    "run_chicane",
    "seqinfo",
    "shiftRegions",
    "show",
    "showLinkSet",
    "subsetBait",
    "subsetBaitRegion",
    "subsetOE",
    "themeLinkset",
    "themeRange",
    "trim",
    "unchecked_regions<-",
    "width",
    "withTxDb"
  ],
  "_datasets": [
    {
      "name": "linkExample",
      "title": "Example linkSet Object",
      "object": "linkExample",
      "file": "linkExample.rda",
      "class": [
        "linkSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "annotateInter-linkSet-method",
      "title": "Annotate linkSet with inter/intra chromosome interactions",
      "topics": [
        "annotateInter",
        "annotateInter,linkSet-method"
      ]
    },
    {
      "page": "annotatePromoter-linkSet-method",
      "title": "Annotate the link set with txDb. Give a gene list, and return a",
      "topics": [
        "annotatePromoter",
        "annotatePromoter,linkSet-method"
      ]
    },
    {
      "page": "as.data.frame-linkSet-method",
      "title": "coerce linkSet to DataFrame",
      "topics": [
        "as.data.frame,linkSet-method"
      ]
    },
    {
      "page": "as.GInteractions",
      "title": "Convert to GInteractions",
      "topics": [
        "as.GInteractions",
        "as.GInteractions,linkSet-method"
      ]
    },
    {
      "page": "linkSet-accessors",
      "title": "linkSet-accessors",
      "topics": [
        "$",
        "$,linkSet-method",
        "$<-,linkSet-method",
        "anchor1",
        "anchor1,linkSet-method",
        "anchor1<-",
        "anchor2",
        "anchor2,linkSet-method",
        "anchor2<-",
        "anchorIds",
        "anchorIds,linkSet-method",
        "anchors",
        "anchors,linkSet-method",
        "bait",
        "bait,linkSet-method",
        "bait<-",
        "bait<-,linkSet-method",
        "first",
        "first,linkSet-method",
        "names",
        "names,linkSet-method",
        "names<-",
        "names<-,linkSet-method",
        "oe",
        "oe,linkSet-method",
        "oe<-,linkSet-method",
        "regions",
        "regions,linkSet-method",
        "regions<-",
        "regions<-,linkSet-method",
        "regionsBait",
        "regionsBait,linkSet-method",
        "regionsBait<-,linkSet-method",
        "second",
        "second,linkSet-method",
        "seqinfo",
        "seqinfo,linkSet-method",
        "unchecked_anchor1",
        "unchecked_anchor1<-,linkSet-method",
        "unchecked_anchor2",
        "unchecked_anchor2<-,linkSet-method",
        "unchecked_regions",
        "unchecked_regions<-",
        "unchecked_regions<-,linkSet-method"
      ]
    },
    {
      "page": "baitGInteractions",
      "title": "Convert GInteractions to linkSet with bait annotations",
      "topics": [
        "baitGInteractions",
        "baitGInteractions,GInteractions,GRanges,GRanges-method"
      ]
    },
    {
      "page": "character_Or_missing-class",
      "title": "Character or Missing Class Union",
      "topics": [
        "character_Or_missing-class"
      ]
    },
    {
      "page": "cleanUnusedRegions",
      "title": "Clean Unused Regions",
      "topics": [
        "cleanUnusedRegions",
        "cleanUnusedRegions,linkSet-method",
        "clean_unused_regions",
        "clean_unused_regions,linkSet-method"
      ]
    },
    {
      "page": "Convert",
      "title": "Convert GInteractions to linkSet",
      "topics": [
        "Convert",
        "Convert,ANY-method",
        "Convert,data.frame-method",
        "Convert,GInteractions-method",
        "Convert,Pairs-method",
        "readvalidPairs"
      ]
    },
    {
      "page": "countInteractibility",
      "title": "Count bait and oe interactibility",
      "topics": [
        "countInteractibility",
        "countInteractibility,linkSet-method"
      ]
    },
    {
      "page": "countInteractions",
      "title": "Count Bait and Other End Interactions",
      "topics": [
        "countBaitOe",
        "countInteractions",
        "countInteractions,linkSet-method"
      ]
    },
    {
      "page": "crossGeneEnhancer-linkSet-method",
      "title": "Cross gene enhancer",
      "topics": [
        "crossGeneEnhancer",
        "crossGeneEnhancer,linkSet-method"
      ]
    },
    {
      "page": "diagnoseLinkSet-linkSet-method",
      "title": "Diagnose the linkSet object, return barplot of inter/intra interaction and distance distribution",
      "topics": [
        "diagnoseLinkSet",
        "diagnoseLinkSet,linkSet-method"
      ]
    },
    {
      "page": "Embryo_body",
      "title": "Embryo Body BED File",
      "topics": [
        "Embryo_body"
      ]
    },
    {
      "page": "exportInterBed",
      "title": "Export linkSet to interBed format",
      "topics": [
        "exportInterBed",
        "exportInterBed,linkSet-method"
      ]
    },
    {
      "page": "exportWashU",
      "title": "Export linkSet to WashU browser format",
      "topics": [
        "exportWashU",
        "exportWashU,linkSet-method"
      ]
    },
    {
      "page": "filterLinks-linkSet-method",
      "title": "Filter links for further analysis",
      "topics": [
        "filterLinks",
        "filterLinks,linkSet-method"
      ]
    },
    {
      "page": "geom_linkset",
      "title": "Add Genome Links to Coverage Plot",
      "topics": [
        "geom_linkset",
        "geom_linkset,linkSet-method"
      ]
    },
    {
      "page": "linkExample",
      "title": "Example linkSet Object",
      "topics": [
        "linkExample"
      ]
    },
    {
      "page": "linkSet",
      "title": "linkSet: Base Classes for Storing Genomic Link Data",
      "topics": [
        "linkSet"
      ]
    },
    {
      "page": "linkSet-class",
      "title": "LinkSet object",
      "topics": [
        "LinkSet",
        "linkSet-class"
      ]
    },
    {
      "page": "linkSet-character-GRanges-character_Or_missing-method",
      "title": "Create a linkSet object from input data",
      "topics": [
        "linkSet,character,GRanges,character_Or_missing-method"
      ]
    },
    {
      "page": "linkSet-GRanges-GRanges-character_Or_missing-method",
      "title": "Create a linkSet object from input data",
      "topics": [
        "linkSet,GRanges,GRanges,character_Or_missing-method"
      ]
    },
    {
      "page": "oe-set",
      "title": "Set Other End (OE) Anchors",
      "topics": [
        "oe<-"
      ]
    },
    {
      "page": "orderLinks-linkSet-method",
      "title": "Order linkSet by mcols",
      "topics": [
        "orderLinks",
        "orderLinks,linkSet-method"
      ]
    },
    {
      "page": "pairdist-linkSet-method",
      "title": "Calculate the distance between bait and the other end",
      "topics": [
        "pairdist",
        "pairdist,linkSet-method"
      ]
    },
    {
      "page": "plotBaits",
      "title": "Plot Baits",
      "topics": [
        "plotBaits"
      ]
    },
    {
      "page": "plotGenomicRanges",
      "title": "Plot Genomic Ranges",
      "topics": [
        "plotGenomicRanges",
        "plot_genomic_ranges",
        "plot_genomic_ranges,linkSet-method"
      ]
    },
    {
      "page": "plotGenomicRanges-linkSet-method",
      "title": "Plot genomic ranges for linkSet objects",
      "topics": [
        "plotGenomicRanges,linkSet-method"
      ]
    },
    {
      "page": "reduceRegions",
      "title": "Reduce Regions in a linkSet Object",
      "topics": [
        "reduceRegions",
        "reduceRegions,linkSet-method"
      ]
    },
    {
      "page": "regionsBait-set",
      "title": "Set Bait Regions",
      "topics": [
        "regionsBait<-"
      ]
    },
    {
      "page": "run_chicane",
      "title": "Run ChICANE Analysis",
      "topics": [
        "run_chicane",
        "run_chicane,linkSet-method"
      ]
    },
    {
      "page": "show",
      "title": "Display detailed information about a linkSet object",
      "topics": [
        "show,linkSet-method"
      ]
    },
    {
      "page": "showLinkSet",
      "title": "Show linkSet Object Details",
      "topics": [
        "showLinkSet",
        "showLinkSet,linkSet-method"
      ]
    },
    {
      "page": "linkSet-subset-methods",
      "title": "Subset linkSet object based on bait names",
      "topics": [
        "subsetBait",
        "subsetBait,linkSet-method",
        "subsetBaitRegion",
        "subsetBaitRegion,linkSet-method",
        "subsetOE",
        "subsetOE,linkSet-method"
      ]
    },
    {
      "page": "themeLinkset",
      "title": "Theme for linkSet plots",
      "topics": [
        "themeLinkset"
      ]
    },
    {
      "page": "themeRange",
      "title": "Theme for genomic range plots",
      "topics": [
        "themeRange"
      ]
    },
    {
      "page": "linkSet-GRange-Methods",
      "title": "linkSet-GRange-Methods",
      "topics": [
        "flank",
        "flank,linkSet-method",
        "flankRegions",
        "flankRegions,linkSet-method",
        "narrow",
        "narrow,linkSet-method",
        "narrowRegions",
        "narrowRegions,linkSet-method",
        "promoterRegions",
        "promoterRegions,linkSet-method",
        "promoters",
        "promoters,linkSet-method",
        "reduce",
        "reduce,linkSet-method",
        "resize",
        "resize,linkSet-method",
        "resizeRegions",
        "resizeRegions,linkSet-method",
        "shift",
        "shift,linkSet-method",
        "shiftRegions",
        "shiftRegions,linkSet-method",
        "trim",
        "trim,linkSet-method",
        "width",
        "width,linkSet-method"
      ]
    },
    {
      "page": "withTxDb",
      "title": "Database Operation with Connection Management",
      "topics": [
        "withTxDb",
        "withTxDb,character,function-method"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/linkSet/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/linkSet/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "askpass",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
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