{
  "_id": "6a1b00a91d7bb097a09ffb4a",
  "Package": "trackViewer",
  "Type": "Package",
  "Title": "A R/Bioconductor package with web interface for drawing elegant\ninteractive tracks or lollipop plot to facilitate integrated\nanalysis of multi-omics data",
  "Version": "1.49.0",
  "Authors@R": "c(person(given=\"Jianhong\", family=\"Ou\", email=\"jou@morgridge.org\", \nrole=c(\"aut\", \"cre\"), comment=c(ORCID=\"0000-0002-8652-2488\")),\nperson(given=\"Julie Lihua\", family=\"Zhu\",\nrole=\"aut\", email=\"Julie.Zhu@umassmed.edu\"))",
  "Maintainer": "Jianhong Ou <jou@morgridge.org>",
  "Description": "Visualize mapped reads along with annotation as track\nlayers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq,\nDNA-seq, SNPs and methylation data.",
  "License": "GPL (>= 2)",
  "biocViews": "Visualization",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:35 UTC",
  "RemoteUrl": "https://github.com/bioc/trackViewer",
  "RemoteRef": "HEAD",
  "RemoteSha": "ea7da89d27c3c123f98fcd043e958c269a1a997b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:52:54 UTC",
    "User": "root"
  },
  "Author": "Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>),\nJulie Lihua Zhu [aut]",
  "MD5sum": "68fa087c34d10e144542e6ec370fb6c6",
  "_user": "bioc",
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  "_created": "2026-05-30T09:52:54.000Z",
  "_published": "2026-05-30T15:22:17.868Z",
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    "warning": 3,
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676370902",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/trackViewer",
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    "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_23 branch\n",
    "time": 1777379915
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  "_maintainer": {
    "name": "Jianhong Ou",
    "email": "jou@morgridge.org",
    "orcid": "0000-0002-8652-2488"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
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      "role": "Depends"
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      "package": "grDevices",
      "role": "Depends"
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    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "grid",
      "role": "Depends"
    },
    {
      "package": "Seqinfo",
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    },
    {
      "package": "GenomeInfoDb",
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    },
    {
      "package": "GenomicAlignments",
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      "package": "GenomicFeatures",
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    },
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      "package": "Gviz",
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      "package": "Rsamtools",
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    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
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    },
    {
      "package": "BiocGenerics",
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    },
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    },
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      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
      "role": "Suggests"
    },
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      "package": "org.Hs.eg.db",
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      "package": "htmltools",
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      "package": "rmarkdown",
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      "package": "motifStack",
      "role": "Suggests"
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  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 3,
  "_updates": [
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      "week": "2025-25",
      "n": 1
    },
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  "_tags": [],
  "_bioc": [
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      "branch": "devel",
      "version": "1.49.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.48.0",
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  "_topics": [
    "visualization"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 1294,
    "source": "https://www.bioconductor.org/packages/stats/bioc/trackViewer"
  },
  "_mentions": 14,
  "_searchresults": 227,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/trackViewer.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/jianhong/trackviewer",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addArrowMark",
    "addGuideLine",
    "addInteractionAnnotation",
    "ARA",
    "browseTracks",
    "browseTracksOutput",
    "coverageGR",
    "dandelion.plot",
    "geneModelFromTxdb",
    "geneTrack",
    "getCurTrackViewport",
    "getGeneIDsFromTxDb",
    "getLocation",
    "gi2track",
    "gieStain",
    "GIoperator",
    "GRoperator",
    "ideogramPlot",
    "importBam",
    "importData",
    "importGInteractions",
    "importScore",
    "listChromosomes",
    "listNormalizations",
    "listResolutions",
    "loadIdeogram",
    "lolliplot",
    "optimizeStyle",
    "parse2GRanges",
    "parseWIG",
    "plotGRanges",
    "reduce",
    "renderbrowseTracks",
    "seqlevels",
    "seqlevelsStyle",
    "seqlevelsStyle<-",
    "setTrackStyleParam",
    "setTrackViewerStyleParam",
    "setTrackXscaleParam",
    "setTrackYaxisParam",
    "show",
    "trackList",
    "trackViewerStyle",
    "viewGene",
    "viewTracks"
  ],
  "_help": [
    {
      "page": "trackViewer-package",
      "title": "Minimal designed plotting tool for genomic data",
      "topics": [
        "trackViewer-package",
        "trackViewer"
      ]
    },
    {
      "page": "addArrowMark",
      "title": "Add arrow mark to the figure at a given position",
      "topics": [
        "addArrowMark"
      ]
    },
    {
      "page": "addGuideLine",
      "title": "Add guide lines to the tracks",
      "topics": [
        "addGuideLine"
      ]
    },
    {
      "page": "addInteractionAnnotation",
      "title": "Add annotation markers to the figure at a given position",
      "topics": [
        "addInteractionAnnotation"
      ]
    },
    {
      "page": "ARA",
      "title": "Aggregate Region Analysis",
      "topics": [
        "ARA"
      ]
    },
    {
      "page": "browseTracks",
      "title": "browse tracks",
      "topics": [
        "browseTracks"
      ]
    },
    {
      "page": "browseTracks-shiny",
      "title": "Shiny bindings for browseTracks",
      "topics": [
        "browseTracks-shiny",
        "browseTracksOutput",
        "renderbrowseTracks"
      ]
    },
    {
      "page": "coverageGR",
      "title": "calculate coverage",
      "topics": [
        "coverageGR"
      ]
    },
    {
      "page": "dandelion.plot",
      "title": "dandelion.plots",
      "topics": [
        "dandelion.plot"
      ]
    },
    {
      "page": "geneModelFromTxdb",
      "title": "Prepare gene model from an object of TxDb",
      "topics": [
        "geneModelFromTxdb"
      ]
    },
    {
      "page": "geneTrack",
      "title": "track from TxDb",
      "topics": [
        "geneTrack"
      ]
    },
    {
      "page": "getCurTrackViewport",
      "title": "Get current track viewport",
      "topics": [
        "getCurTrackViewport"
      ]
    },
    {
      "page": "getGeneIDsFromTxDb",
      "title": "get gene ids by genomic location",
      "topics": [
        "getGeneIDsFromTxDb"
      ]
    },
    {
      "page": "getLocation",
      "title": "get genomic location by gene symbol",
      "topics": [
        "getLocation"
      ]
    },
    {
      "page": "gi2track",
      "title": "convert GInteractions to track object",
      "topics": [
        "gi2track"
      ]
    },
    {
      "page": "gieStain",
      "title": "color sheme for the schema for Chromosome Band (Ideogram)",
      "topics": [
        "gieStain"
      ]
    },
    {
      "page": "GIoperator",
      "title": "GInteractions operator",
      "topics": [
        "GIoperator"
      ]
    },
    {
      "page": "gridPlot",
      "title": "plot GRanges metadata",
      "topics": [
        "gridPlot"
      ]
    },
    {
      "page": "GRoperator",
      "title": "GRanges operator",
      "topics": [
        "GRoperator"
      ]
    },
    {
      "page": "ideogramPlot",
      "title": "plot ideogram with data",
      "topics": [
        "ideogramPlot"
      ]
    },
    {
      "page": "importBam",
      "title": "Reading data from a BAM file",
      "topics": [
        "importBam"
      ]
    },
    {
      "page": "importData",
      "title": "Reading data from a BED or WIG file to RleList",
      "topics": [
        "importData"
      ]
    },
    {
      "page": "importGInteractions",
      "title": "Reading data from a ginteractions, hic, cool, or validPairs file",
      "topics": [
        "importGInteractions"
      ]
    },
    {
      "page": "importScore",
      "title": "Reading data from a BED or WIG file",
      "topics": [
        "importScore"
      ]
    },
    {
      "page": "importScSeqScore",
      "title": "plot tracks for single cell RNAseq",
      "topics": [
        "importScSeqScore"
      ]
    },
    {
      "page": "listChromosomes",
      "title": "List the available chromosome",
      "topics": [
        "listChromosomes"
      ]
    },
    {
      "page": "listNormalizations",
      "title": "List the available normalizations",
      "topics": [
        "listNormalizations"
      ]
    },
    {
      "page": "listResolutions",
      "title": "List the available resolutions",
      "topics": [
        "listResolutions"
      ]
    },
    {
      "page": "loadIdeogram",
      "title": "load ideogram from UCSC",
      "topics": [
        "loadIdeogram"
      ]
    },
    {
      "page": "lolliplot",
      "title": "Lolliplots",
      "topics": [
        "lolliplot"
      ]
    },
    {
      "page": "optimizeStyle",
      "title": "Optimize the style of plot",
      "topics": [
        "optimizeStyle"
      ]
    },
    {
      "page": "parse2GRanges",
      "title": "parse text into GRanges",
      "topics": [
        "parse2GRanges"
      ]
    },
    {
      "page": "parseWIG",
      "title": "convert WIG format track to BED format track",
      "topics": [
        "parseWIG"
      ]
    },
    {
      "page": "plotGRanges",
      "title": "plot GRanges data",
      "topics": [
        "plotGRanges"
      ]
    },
    {
      "page": "plotIdeo",
      "title": "plot ideogram",
      "topics": [
        "plotIdeo"
      ]
    },
    {
      "page": "plotOneIdeo",
      "title": "plot ideogram with data for one chromosome",
      "topics": [
        "plotOneIdeo"
      ]
    },
    {
      "page": "pos-class",
      "title": "Class '\"pos\"'",
      "topics": [
        "pos",
        "pos-class"
      ]
    },
    {
      "page": "reduce-GInteractions-method",
      "title": "Reduce method for 'GInteractions'",
      "topics": [
        "reduce,GInteractions",
        "reduce,GInteractions-method"
      ]
    },
    {
      "page": "trackList-class",
      "title": "List of tracks",
      "topics": [
        "seqlevelsStyle<-,trackList-method",
        "trackList",
        "trackList-class"
      ]
    },
    {
      "page": "trackStyle-class",
      "title": "Class '\"trackStyle\"'",
      "topics": [
        "$,track-method",
        "$,trackStyle-method",
        "$<-,track-method",
        "$<-,trackStyle-method",
        "seqlevels,track-method",
        "seqlevelsStyle,track-method",
        "seqlevelsStyle<-,track-method",
        "setTrackStyleParam",
        "setTrackStyleParam,track,character,ANY-method",
        "setTrackStyleParam,track,character-method",
        "setTrackXscaleParam",
        "setTrackXscaleParam,track,character,ANY-method",
        "setTrackXscaleParam,track,character-method",
        "setTrackYaxisParam",
        "setTrackYaxisParam,track,character,ANY-method",
        "setTrackYaxisParam,track,character-method",
        "show,track-method",
        "track",
        "track-class",
        "trackStyle",
        "trackStyle-class"
      ]
    },
    {
      "page": "trackViewerStyle-class",
      "title": "Class '\"trackViewerStyle\"'",
      "topics": [
        "setTrackViewerStyleParam",
        "setTrackViewerStyleParam,trackViewerStyle,character,ANY-method",
        "setTrackViewerStyleParam,trackViewerStyle,character-method",
        "trackViewerStyle",
        "trackViewerStyle-class"
      ]
    },
    {
      "page": "viewGene",
      "title": "plot tracks based on gene name",
      "topics": [
        "viewGene"
      ]
    },
    {
      "page": "viewTracks",
      "title": "plot the tracks",
      "topics": [
        "viewTracks"
      ]
    },
    {
      "page": "xscale-class",
      "title": "Class '\"xscale\"'",
      "topics": [
        "xscale",
        "xscale-class"
      ]
    },
    {
      "page": "yaxisStyle-class",
      "title": "Class '\"yaxisStyle\"'",
      "topics": [
        "yaxisStyle",
        "yaxisStyle-class"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/trackViewer/raw/HEAD/README.md",
  "_rundeps": [
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    "AnnotationDbi",
    "AnnotationFilter",
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    "Rhdf5lib",
    "Rhtslib",
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    "RSQLite",
    "rstudioapi",
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    "S4Vectors",
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    "SummarizedExperiment",
    "sys",
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    "tinytex",
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    "UCSC.utils",
    "utf8",
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    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "changeTracksStyles.Rmd",
      "filename": "changeTracksStyles.html",
      "title": "trackViewer Vignette: change the track styles",
      "author": "Jianhong Ou, Lihua Julie Zhu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Prepare toy data",
        "Using the browseTracks function as a helper",
        "Adjust the x-axis or the X scale",
        "Adjust the y-axis",
        "Adjust the label of y-axis",
        "Adjust the track color",
        "Adjust the track height",
        "Change the track names",
        "Show paired data in the same track",
        "Show signals and the called peaks",
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        "Session Info"
      ],
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      "title": "trackViewer Vignette: dandelionPlot",
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      "engine": "knitr::rmarkdown",
      "headings": [
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        "Change the type of Dandelion plot",
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      "title": "trackViewer Vignette: lollipopPlot",
      "author": "Jianhong Ou, Lihua Julie Zhu",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Change the lolliplot color",
        "Change the color of the features.",
        "Change the color and opacity of the lollipop.",
        "Add the index labels in the node",
        "Change the height of the features",
        "Plot multiple transcripts in the features",
        "Change the height of a lollipop plot",
        "Customize the x-axis label position",
        "Customize the y-axis label position",
        "Jitter the label",
        "Add a legend",
        "Control the labels",
        "Change the lolliplot type",
        "Change the shape for \"circle\" plot",
        "Google pin",
        "Flag",
        "Pie plot",
        "Plot multiple samples",
        "Multiple layers",
        "pie.stack layout",
        "Caterpillar layout",
        "EMBL-EBI Proteins API",
        "Variant Call Format (VCF) data",
        "Methylation data",
        "Change the node size",
        "Change the scale of the x-axis (xscale)",
        "Split the lollipop plot into multiLayers",
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      "author": "Jianhong Ou, Lihua Julie Zhu",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Browse",
        "Steps of using trackViewer \\Biocpkg",
        "Step 1. Import data",
        "Step 2. Build the gene model",
        "Step 3. View the tracks",
        "Generate and edit an interactive plot using the browseTracks function",
        "Plot multiple genes in one track",
        "Operators",
        "Lolliplot",
        "Dandelion Plot",
        "Plot chromatin interactions data",
        "Ideogram Plot",
        "Web application of trackViewer",
        "Session Info"
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      "title": "trackViewer Vignette: plot interaction data",
      "author": "Jianhong Ou, Lihua Julie Zhu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Plot chromatin interactions data in linear layout",
        "Session Info"
      ],
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      "modified": "2024-11-08 14:45:12",
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