{
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  "Package": "igvShiny",
  "Title": "igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an\ninteractive tool for visualization and exploration integrated\ngenomic data)",
  "Version": "1.9.51",
  "Date": "2026-09-30",
  "Authors@R": "c(\nperson(\"Paul\",\"Shannon\", role = c(\"aut\"),\nemail = \"paul.thurmond.shannon@gmail.com\"),\nperson(\"Arkadiusz\", \"Gladki\", role=c(\"aut\", \"cre\"),\nemail=\"gladki.arkadiusz@gmail.com\", comment = c(ORCID = \"0000-0002-7059-6378\")),\nperson(\"Karolina\",\"Scigocka\", role = c(\"aut\"),\nemail = \"scigocka.karolina@gmail.com\"),\nperson(\"Carolina\", \"Heimann\", role = c(\"ctb\"),\nemail = \"carolina.heimann@gmail.com\"),\nperson(\"Steffen\", \"Klasberg\", role = c(\"ctb\"),\nemail = \"klasberg@dkms-lab.de\"),\nperson(\"Vincent\", \"Carey\", role = c(\"ctb\"),\nemail = \"stvjc@channing.harvard.edu\"),\nperson(\"Parv\", \"Sachdeva\", role = c(\"ctb\"),\nemail = \"parv.sachdeva@sonomabio.com\"),\nperson(\"Mateusz\", \"Gladki\", role = c(\"ctb\"),\nemail = \"gladkiimateusz@gmail.com\"),\nperson(\"R Consortium\", role = \"fnd\")\n)",
  "Description": "This package is a wrapper of Integrative Genomics Viewer\n(IGV). It comprises an htmlwidget version of IGV. It can be\nused as a module in Shiny apps.",
  "URL": "https://github.com/gladkia/igvShiny,\nhttps://gladkia.github.io/igvShiny/",
  "BugReports": "https://github.com/gladkia/igvShiny/issues",
  "biocViews": "Software, ShinyApps, Sequencing, Coverage",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Collate": "'constants.R' 'genomeSpec.R' 'referenceCheck.R' 'GWASTrack.R'\n'rangeServer.R' 'igvShiny.R' 'packages.R' 'utils.R' 'zzz.R'",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-09-29 23:50:39 UTC",
  "RemoteUrl": "https://github.com/bioc/igvShiny",
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  "Packaged": {
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  "Author": "Paul Shannon [aut],\nArkadiusz Gladki [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-7059-6378>),\nKarolina Scigocka [aut],\nCarolina Heimann [ctb],\nSteffen Klasberg [ctb],\nVincent Carey [ctb],\nParv Sachdeva [ctb],\nMateusz Gladki [ctb],\nR Consortium [fnd]",
  "Maintainer": "Arkadiusz Gladki <gladki.arkadiusz@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "igvShiny_1.9.51.tar.gz",
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  "_created": "2026-09-30T06:58:26.000Z",
  "_published": "2026-09-30T07:05:28.507Z",
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    "message": "chore(demo): pin Connect Cloud manifest to 1.9.51 (a61d604) (#194)",
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  "_exports": [
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    "display",
    "get_basic_genomes",
    "get_cas_genomes",
    "get_css_genomes",
    "get_tracks_dir",
    "getGenomicRegion",
    "getUrl",
    "GWASTrack",
    "igvShiny",
    "igvShinyOutput",
    "loadBamTrackFromLocalData",
    "loadBamTrackFromLocalFile",
    "loadBamTrackFromURL",
    "loadBedGraphTrack",
    "loadBedGraphTrackFromURL",
    "loadBedTrack",
    "loadCramTrackFromLocalData",
    "loadCramTrackFromLocalFile",
    "loadCramTrackFromURL",
    "loadGFF3TrackFromLocalData",
    "loadGFF3TrackFromURL",
    "loadGwasTrack",
    "loadSegTrack",
    "loadSpliceJunctionTrackFromLocalData",
    "loadSpliceJunctionTrackFromURL",
    "loadVcfTrack",
    "parseAndValidateGenomeSpec",
    "removeTracksByName",
    "removeUserAddedTracks",
    "renderIgvShiny",
    "serveLocalFile",
    "show",
    "showGenomicRegion"
  ],
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      "page": "dot-packJunctionAttributes",
      "title": "Pack junction attributes into a bed name column",
      "topics": [
        ".packJunctionAttributes"
      ]
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    {
      "page": "dot-sanitizeAndMergeOptions",
      "title": "Sanitize and merge track configuration options",
      "topics": [
        ".sanitizeAndMergeOptions"
      ]
    },
    {
      "page": "dot-sanitizeChromosomeColorMap",
      "title": "Check a chromosome color map before it reaches igv.js",
      "topics": [
        ".sanitizeChromosomeColorMap"
      ]
    },
    {
      "page": "dot-sanitizeTrack",
      "title": "Sanitize one startup track specification",
      "topics": [
        ".sanitizeTrack"
      ]
    },
    {
      "page": "dot-sanitizeTracks",
      "title": "Sanitize a list of startup track specifications",
      "topics": [
        ".sanitizeTracks"
      ]
    },
    {
      "page": "checkReferenceCompatibility",
      "title": "Check reference compatibility between track data and genome specification",
      "topics": [
        "checkReferenceCompatibility"
      ]
    },
    {
      "page": "display",
      "title": "display the already constructed and configured track",
      "topics": [
        "display",
        "display,GWASTrack-method"
      ]
    },
    {
      "page": "get_basic_genomes",
      "title": "get_basic_genomes",
      "topics": [
        "get_basic_genomes"
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    {
      "page": "get_cas_genomes",
      "title": "get_cas_genomes",
      "topics": [
        "get_cas_genomes"
      ]
    },
    {
      "page": "get_css_genomes",
      "title": "get_css_genomes",
      "topics": [
        "get_css_genomes"
      ]
    },
    {
      "page": "get_tracks_dir",
      "title": "get_tracks_dir Get the directory where tracks are stored. The directory can be defined with environmental variable. If not defined the default is a directory called \"tracks\" in the temp directory. We need a local directory to write files - for instance, a vcf file representing a genomic region of interest. We then tell shiny about that directory, so that shiny's built-in http server can serve up files we write there, ultimately consumed by igv.js",
      "topics": [
        "get_tracks_dir"
      ]
    },
    {
      "page": "getUrl",
      "title": "the url of the gwas table",
      "topics": [
        "getUrl",
        "getUrl,GWASTrack-method"
      ]
    },
    {
      "page": "GWASTrack-class",
      "title": "Constructor for GWASTrack",
      "topics": [
        ".GWASTrack",
        "GWASTrack",
        "GWASTrack-class"
      ]
    },
    {
      "page": "igvShiny",
      "title": "Create an igvShiny instance",
      "topics": [
        "igvShiny"
      ]
    },
    {
      "page": "igvShinyOutput",
      "title": "create the UI for the widget",
      "topics": [
        "igvShinyOutput"
      ]
    },
    {
      "page": "loadBamTrackFromLocalData",
      "title": "load GenomicAlignments data as an igv.js alignment track",
      "topics": [
        "loadBamTrackFromLocalData"
      ]
    },
    {
      "page": "loadBamTrackFromLocalFile",
      "title": "Load a BAM Track from a Local File via HTTP Range Requests",
      "topics": [
        "loadBamTrackFromLocalFile"
      ]
    },
    {
      "page": "loadBamTrackFromURL",
      "title": "load a bam track which, with index, is served up by http",
      "topics": [
        "loadBamTrackFromURL"
      ]
    },
    {
      "page": "loadGenomeAnnotationTrack",
      "title": "load a scored genome annotation track provided as a data.frame",
      "topics": [
        "loadBedGraphTrack",
        "loadGenomeAnnotationTrack"
      ]
    },
    {
      "page": "loadBedGraphTrackFromURL",
      "title": "load a bedgraph track from a URL",
      "topics": [
        "loadBedGraphTrackFromURL"
      ]
    },
    {
      "page": "loadBedTrack",
      "title": "load a bed track provided as a data.frame",
      "topics": [
        "loadBedTrack"
      ]
    },
    {
      "page": "loadCramTrackFromLocalData",
      "title": "load a cram file sitting on the same machine as the shiny app",
      "topics": [
        "loadCramTrackFromLocalData",
        "loadCramTrackFromLocalFile"
      ]
    },
    {
      "page": "loadCramTrackFromURL",
      "title": "load a cram track which, with index, is served up by http",
      "topics": [
        "loadCramTrackFromURL"
      ]
    },
    {
      "page": "loadGFF3TrackFromLocalData",
      "title": "load a GFF3 track defined by local data",
      "topics": [
        "loadGFF3TrackFromLocalData"
      ]
    },
    {
      "page": "loadGFF3TrackFromURL",
      "title": "load a GFF3 track which, with index, is served up by http",
      "topics": [
        "loadGFF3TrackFromURL"
      ]
    },
    {
      "page": "loadGwasTrack",
      "title": "load a GWAS (genome-wide association study) track provided as a data.frame",
      "topics": [
        "loadGwasTrack"
      ]
    },
    {
      "page": "loadSEGTrack",
      "title": "load a seg track provided as a data.frame",
      "topics": [
        "loadSEGTrack",
        "loadSegTrack"
      ]
    },
    {
      "page": "loadSpliceJunctionTrackFromLocalData",
      "title": "load a splice junction track from a data.frame",
      "topics": [
        "loadSpliceJunctionTrackFromLocalData"
      ]
    },
    {
      "page": "loadSpliceJunctionTrackFromURL",
      "title": "load a splice junction track served up by http",
      "topics": [
        "loadSpliceJunctionTrackFromURL"
      ]
    },
    {
      "page": "loadVcfTrack",
      "title": "load a VCF (variant) track provided as a Bioconductor VariantAnnotation object",
      "topics": [
        "loadVcfTrack"
      ]
    },
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      "page": "parseAndValidateGenomeSpec",
      "title": "parseAndValidateGenomeSpec",
      "topics": [
        "parseAndValidateGenomeSpec"
      ]
    },
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      "page": "removeTracksByName",
      "title": "remove tracks from the browser",
      "topics": [
        "removeTracksByName"
      ]
    },
    {
      "page": "removeUserAddedTracks",
      "title": "remove only those tracks explicitly added by your app",
      "topics": [
        "removeUserAddedTracks"
      ]
    },
    {
      "page": "renderIgvShiny",
      "title": "draw the igv genome browser element",
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        "renderIgvShiny"
      ]
    },
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      "title": "Serve a local file via HTTP Range Requests from the Shiny session",
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        "serveLocalFile"
      ]
    },
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      "title": "Display a short summary of a GWASTrack object",
      "topics": [
        "show,GWASTrack-method"
      ]
    },
    {
      "page": "showGenomicRegion",
      "title": "focus igv on a region",
      "topics": [
        "getGenomicRegion",
        "showGenomicRegion"
      ]
    }
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      "title": "Getting started with igvShiny",
      "author": "Arkadiusz Gladki",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Install",
        "The three moving parts",
        "A complete app",
        "Loading a track from your own data",
        "Loading tracks at startup",
        "Drawing two tracks in one panel",
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      "created": "2026-07-25 15:11:48",
      "modified": "2026-08-01 09:27:40",
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    {
      "source": "track-options.Rmd",
      "filename": "track-options.html",
      "title": "Track options reference",
      "author": "Arkadiusz Gladki",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What this vignette is",
        "How an option reaches the browser",
        "Loaders",
        "Options every track accepts",
        "Numeric tracks: bedGraph, wig, bigWig",
        "Annotation tracks: bed, gff3",
        "Alignment tracks: bam, cram",
        "Variant tracks: vcf",
        "GWAS tracks",
        "Splice junction tracks",
        "Options on startup tracks",
        "When an option seems to do nothing",
        "Session Info"
      ],
      "created": "2026-07-31 05:54:08",
      "modified": "2026-09-11 06:04:41",
      "commits": 3
    }
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  "_universes": [
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    "gladkia"
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