{
  "_id": "6a1be20b1d7bb097a0a18951",
  "Package": "igvR",
  "Type": "Package",
  "Title": "igvR: integrative genomics viewer",
  "Version": "1.33.2",
  "Date": "2023-10-09",
  "Authors@R": "c(\nperson(\"Paul\", \"Shannon\", role = \"aut\"),\nperson(\"Arkadiusz\", \"Gladki\", email = \"gladki.arkadiusz@gmail.com\",\nrole = c(\"aut\", \"cre\"))\n)",
  "Description": "Access to igv.js, the Integrative Genomics Viewer running\nin a web browser.",
  "URL": "https://gladkia.github.io/igvR/",
  "License": "MIT + file LICENSE",
  "LazyLoad": "yes",
  "biocViews": "Visualization, ThirdPartyClient, GenomeBrowsers",
  "Collate": "'Track.R' 'igvAnnotationTrack.R' 'UCSCBedAnnotationTrack.R'\n'DataFrameAnnotationTrack.R' 'VariantTrack.R'\n'QuantitativeTrack.R' 'DataFrameQuantitativeTrack.R'\n'UCSCBedGraphQuantitativeTrack.R' 'GRangesAnnotationTrack.R'\n'GRangesQuantitativeTrack.R' 'GenomicAlignmentTrack.R'\n'BedpeInteractionsTrack.R' 'RemoteAlignmentTrack.R'\n'GWASTrack.R' 'GWASUrlTrack.R' 'GFF3Track.R' 'genomeSpec.R'\n'igvR.R' 'CramTrack.R'",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-31 06:28:08 UTC",
    "User": "root"
  },
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-01 09:40:03 UTC",
  "RemoteUrl": "https://github.com/bioc/igvR",
  "RemoteRef": "HEAD",
  "RemoteSha": "3dbd016bae0e2ba7de362df75a0f2a6cd050575d",
  "Author": "Paul Shannon [aut],\nArkadiusz Gladki [aut, cre]",
  "Maintainer": "Arkadiusz Gladki <gladki.arkadiusz@gmail.com>",
  "MD5sum": "cdc28838c2f1d08942ee6f0fca82b235",
  "_user": "bioc",
  "_type": "src",
  "_file": "igvR_1.33.2.tar.gz",
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  "_filesize": 7498012,
  "_sha256": "3dc3bc688fa4c27bc859b1077a9d5bd79145388f44f86839913f232f15da45a0",
  "_created": "2026-05-31T06:28:08.000Z",
  "_published": "2026-05-31T07:23:55.633Z",
  "_jobs": [
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  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26705303274",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/igvR",
  "_commit": {
    "id": "3dbd016bae0e2ba7de362df75a0f2a6cd050575d",
    "author": "Arkadiusz Gładki <arek@dobio.link>",
    "committer": "Arkadiusz Gładki <arek@dobio.link>",
    "message": "ci: enable linting in checkPackage (R/ now lint-clean)\n",
    "time": 1777628403
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  "_maintainer": {
    "name": "Arkadiusz Gladki",
    "email": "gladki.arkadiusz@gmail.com",
    "login": "gladkia",
    "linkedin": "in/arkadiusz-gladki-55b94735",
    "twitter": "@biosmooth",
    "description": "",
    "uuid": 41166437
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "GenomicAlignments",
      "role": "Depends"
    },
    {
      "package": "BrowserViz",
      "version": ">= 2.17.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "httpuv",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "VariantAnnotation",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "MotifDb",
      "role": "Suggests"
    },
    {
      "package": "seqLogo",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-51",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 9
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.2",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "visualization",
    "thirdpartyclient",
    "genomebrowsers"
  ],
  "_stars": 45,
  "_contributors": [
    {
      "user": "paul-shannon",
      "count": 278,
      "uuid": 2480712
    },
    {
      "user": "gladkia",
      "count": 42,
      "uuid": 41166437
    },
    {
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      "uuid": 1744257
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    },
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    },
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    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 479,
    "source": "https://www.bioconductor.org/packages/stats/bioc/igvR"
  },
  "_devurl": "https://github.com/gladkia/igvr",
  "_pkgdown": "https://gladkia.github.io/igvR/",
  "_searchresults": 117,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/igvR.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/gladkia/igvr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "BedpeInteractionsTrack",
    "CramTrack",
    "currently.supported.stock.genomes",
    "DataFrameAnnotationTrack",
    "DataFrameQuantitativeTrack",
    "displayTrack",
    "enableMotifLogoPopups",
    "GenomicAlignmentTrack",
    "getGenomicRegion",
    "getSupportedGenomes",
    "getTrackNames",
    "GFF3Track",
    "GRangesAnnotationTrack",
    "GRangesQuantitativeTrack",
    "GWASTrack",
    "GWASUrlTrack",
    "igvR",
    "parseAndValidateGenomeSpec",
    "ping",
    "QuantitativeTrack",
    "RemoteAlignmentTrack",
    "removeTracksByName",
    "saveToSVG",
    "setCustomGenome",
    "setGenome",
    "setTrackClickFunction",
    "setTrackHeight",
    "showGenomicRegion",
    "showTrackLabels",
    "Track",
    "trackInfo",
    "trackSize",
    "UCSCBedAnnotationTrack",
    "UCSCBedGraphQuantitativeTrack",
    "url.exists",
    "VariantTrack",
    "zoomIn",
    "zoomOut"
  ],
  "_help": [
    {
      "page": "BedpeInteractionsTrack-class",
      "title": "Constructor for BedpeInteractionsTrack",
      "topics": [
        ".BedpeInteractionsTrack",
        "BedpeInteractionsTrack",
        "BedpeInteractionsTrack-class"
      ]
    },
    {
      "page": "CramTrack-class",
      "title": "Constructor for CramTrack",
      "topics": [
        ".CramTrack",
        "CramTrack",
        "CramTrack-class"
      ]
    },
    {
      "page": "currently.supported.stock.genomes",
      "title": "currently.supported.stock.genomes",
      "topics": [
        "currently.supported.stock.genomes"
      ]
    },
    {
      "page": "DataFrameAnnotationTrack-class",
      "title": "Constructor for DataFrameAnnotationTrack",
      "topics": [
        ".DataFrameAnnotationTrack",
        "DataFrameAnnotationTrack",
        "DataFrameAnnotationTrack-class"
      ]
    },
    {
      "page": "DataFrameQuantitativeTrack-class",
      "title": "Constructor for DataFrameQuantitativeTrack",
      "topics": [
        ".DataFrameQuantitativeTrack",
        "DataFrameQuantitativeTrack",
        "DataFrameQuantitativeTrack-class"
      ]
    },
    {
      "page": "displayTrack",
      "title": "display the specified track in igv",
      "topics": [
        "displayTrack",
        "displayTrack,igvR-method"
      ]
    },
    {
      "page": "enableMotifLogoPopups",
      "title": "turn mottif log popups on or off",
      "topics": [
        "enableMotifLogoPopups",
        "enableMotifLogoPopups,igvR-method"
      ]
    },
    {
      "page": "GenomicAlignmentTrack-class",
      "title": "Constructor for GenomicAlignmentTrack",
      "topics": [
        ".GenomicAlignmentTrack",
        "GenomicAlignmentTrack",
        "GenomicAlignmentTrack-class"
      ]
    },
    {
      "page": "getGenomicRegion",
      "title": "Obtain the chromosome and coordiates of the currently displayed genomic region.",
      "topics": [
        "getGenomicRegion",
        "getGenomicRegion,igvR-method"
      ]
    },
    {
      "page": "getSupportedGenomes",
      "title": "Get the shorthand codes (eg, \"hg38\") for the genomes currently supported by our use of igv.js",
      "topics": [
        "getSupportedGenomes",
        "getSupportedGenomes,igvR-method"
      ]
    },
    {
      "page": "getTrackNames",
      "title": "Get the names of all the tracks currently displayed in igv",
      "topics": [
        "getTrackNames",
        "getTrackNames,igvR-method"
      ]
    },
    {
      "page": "GFF3Track-class",
      "title": "Constructor for GFF3Track",
      "topics": [
        ".GFF3Track",
        "GFF3Track",
        "GFF3Track-class"
      ]
    },
    {
      "page": "GRangesAnnotationTrack-class",
      "title": "Constructor for GRangesAnnotationTrack",
      "topics": [
        ".GRangesAnnotationTrack",
        "GRangesAnnotationTrack",
        "GRangesAnnotationTrack-class"
      ]
    },
    {
      "page": "GRangesQuantitativeTrack-class",
      "title": "Constructor for GRangesQuantitativeTrack",
      "topics": [
        ".GRangesQuantitativeTrack",
        "GRangesQuantitativeTrack",
        "GRangesQuantitativeTrack-class"
      ]
    },
    {
      "page": "GWASTrack-class",
      "title": "Constructor for GWASTrack",
      "topics": [
        ".GWASTrack",
        ".GWASUrlTrack",
        "GWASTrack",
        "GWASTrack-class"
      ]
    },
    {
      "page": "GWASUrlTrack-class",
      "title": "Constructor for GWASUrlTrack",
      "topics": [
        "GWASUrlTrack"
      ]
    },
    {
      "page": "igvAnnotationTrack-class",
      "title": "Constructor for igvAnnotationTrack",
      "topics": [
        ".igvAnnotationTrack",
        "igvAnnotationTrack",
        "igvAnnotationTrack-class"
      ]
    },
    {
      "page": "igvR-class",
      "title": "Create an igvR object",
      "topics": [
        ".igvR",
        "igvR",
        "igvR-class"
      ]
    },
    {
      "page": "parseAndValidateGenomeSpec",
      "title": "parseAndValidateGenomeSpec",
      "topics": [
        "parseAndValidateGenomeSpec"
      ]
    },
    {
      "page": "ping",
      "title": "Test the connection between your R session and the webapp",
      "topics": [
        "ping",
        "ping,igvR-method"
      ]
    },
    {
      "page": "QuantitativeTrack-class",
      "title": "Constructor for QuantitativeTrack",
      "topics": [
        ".QuantitativeTrack",
        "QuantitativeTrack",
        "QuantitativeTrack-class"
      ]
    },
    {
      "page": "RemoteAlignmentTrack-class",
      "title": "Constructor for RemoteAlignmentTrack",
      "topics": [
        ".RemoteAlignmentTrack",
        "RemoteAlignmentTrack",
        "RemoteAlignmentTrack-class"
      ]
    },
    {
      "page": "removeTracksByName",
      "title": "Remove named tracks",
      "topics": [
        "removeTracksByName",
        "removeTracksByName,igvR-method"
      ]
    },
    {
      "page": "saveToSVG",
      "title": "Get entire igv browser image in svg",
      "topics": [
        "saveToSVG",
        "saveToSVG,igvR-method"
      ]
    },
    {
      "page": "setCustomGenome",
      "title": "Specify the reference genome you wish to use, via full specification of all urls",
      "topics": [
        "setCustomGenome",
        "setCustomGenome,igvR-method"
      ]
    },
    {
      "page": "setGenome",
      "title": "Specify the reference genome, currently limited to hg38, hg19, mm10, tair10.",
      "topics": [
        "setGenome",
        "setGenome,igvR-method"
      ]
    },
    {
      "page": "setTrackClickFunction",
      "title": "Specify (supply) the javascript function run on track click event",
      "topics": [
        "setTrackClickFunction",
        "setTrackClickFunction,igvR-method"
      ]
    },
    {
      "page": "setTrackHeight",
      "title": "Remove named tracks",
      "topics": [
        "setTrackHeight",
        "setTrackHeight,igvR-method"
      ]
    },
    {
      "page": "showGenomicRegion",
      "title": "Set the visible region, by explicit chromLoc string, or by named features in any curently loaded annotation tracks",
      "topics": [
        "showGenomicRegion",
        "showGenomicRegion,igvR-method"
      ]
    },
    {
      "page": "showTrackLabels",
      "title": "Hide or show igv track labels",
      "topics": [
        "showTrackLabels",
        "showTrackLabels,igvR-method"
      ]
    },
    {
      "page": "Track-class",
      "title": "Constructor for Track",
      "topics": [
        ".Track",
        "Track",
        "Track-class"
      ]
    },
    {
      "page": "trackInfo",
      "title": "Get basic info about a track: its type, file format, source and S4 class name",
      "topics": [
        "trackInfo",
        "trackInfo,Track-method"
      ]
    },
    {
      "page": "trackSize-BedpeInteractionsTrack-method",
      "title": "Retrieve the size of the BedpeInteractionsTrack",
      "topics": [
        "trackSize,BedpeInteractionsTrack-method"
      ]
    },
    {
      "page": "trackSize-DataFrameAnnotationTrack-method",
      "title": "Retrieve the size of the DataFrameAnnotationTrack",
      "topics": [
        "trackSize,DataFrameAnnotationTrack-method"
      ]
    },
    {
      "page": "trackSize-DataFrameQuantitativeTrack-method",
      "title": "Retrieve the size of the DataFrameQuantitativeTrack",
      "topics": [
        "trackSize,DataFrameQuantitativeTrack-method"
      ]
    },
    {
      "page": "trackSize-GenomicAlignmentTrack-method",
      "title": "Retrieve the size of the GenomicAlignmentTrack",
      "topics": [
        "trackSize,GenomicAlignmentTrack-method"
      ]
    },
    {
      "page": "trackSize-GFF3Track-method",
      "title": "Retrieve the size of the GFF3Track",
      "topics": [
        "trackSize,GFF3Track-method"
      ]
    },
    {
      "page": "trackSize-GRangesAnnotationTrack-method",
      "title": "Retrieve the size of the GRangesAnnotationTrack",
      "topics": [
        "trackSize,GRangesAnnotationTrack-method"
      ]
    },
    {
      "page": "trackSize-GRangesQuantitativeTrack-method",
      "title": "Retrieve the size of the GRangesQuantitativeTrack",
      "topics": [
        "trackSize,GRangesQuantitativeTrack-method"
      ]
    },
    {
      "page": "trackSize-GWASTrack-method",
      "title": "Retrieve the size of the GWASTrack",
      "topics": [
        "trackSize,GWASTrack-method"
      ]
    },
    {
      "page": "trackSize-GWASUrlTrack-method",
      "title": "Retrieve the size of the GWASUrlTrack",
      "topics": [
        "trackSize,GWASUrlTrack-method"
      ]
    },
    {
      "page": "trackSize",
      "title": "Retrieve the size of the QuantitativeTrack",
      "topics": [
        "trackSize",
        "trackSize,QuantitativeTrack-method"
      ]
    },
    {
      "page": "trackSize-UCSCBedAnnotationTrack-method",
      "title": "Retrieve the size of theUCSCBedAnnotationTrack",
      "topics": [
        "trackSize,UCSCBedAnnotationTrack-method"
      ]
    },
    {
      "page": "trackSize-UCSCBedGraphQuantitativeTrack-method",
      "title": "Retrieve the size of the UCSCBedGraphQuantitativeTrack",
      "topics": [
        "trackSize,UCSCBedGraphQuantitativeTrack-method"
      ]
    },
    {
      "page": "trackSize-VariantTrack-method",
      "title": "Retrieve the size of the VariantTrack",
      "topics": [
        "trackSize,VariantTrack-method"
      ]
    },
    {
      "page": "UCSCBedAnnotationTrack-class",
      "title": "Constructor for UCSCBedAnnotationTrack",
      "topics": [
        ".UCSCBedAnnotationTrack",
        "UCSCBedAnnotationTrack",
        "UCSCBedAnnotationTrack-class"
      ]
    },
    {
      "page": "UCSCBedGraphQuantitativeTrack-class",
      "title": "Constructor for UCSCBedGraphQuantitativeTrack",
      "topics": [
        ".UCSCBedGraphQuantitativeTrack",
        "UCSCBedGraphQuantitativeTrack",
        "UCSCBedGraphQuantitativeTrack-class"
      ]
    },
    {
      "page": "url.exists",
      "title": "url.exists",
      "topics": [
        "url.exists"
      ]
    },
    {
      "page": "VariantTrack-class",
      "title": "Constructor for VariantTrack",
      "topics": [
        "VariantTrack",
        "VariantTrack-class"
      ]
    },
    {
      "page": "zoomIn",
      "title": "zoom the genome view in by a factor of 2",
      "topics": [
        "zoomIn",
        "zoomIn,igvR-method"
      ]
    },
    {
      "page": "zoomOut",
      "title": "zoom the genome view out by a factor of 2",
      "topics": [
        "zoomOut",
        "zoomOut,igvR-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/igvR/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BrowserViz",
    "BSgenome",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DelayedArray",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "httpuv",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "later",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "otel",
    "pkgconfig",
    "png",
    "promises",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "VariantAnnotation",
    "vctrs",
    "XML",
    "XVector",
    "yaml"
  ],
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