{
  "_id": "6a1ad3e41d7bb097a09e3e87",
  "Package": "ggbio",
  "Version": "1.61.0",
  "Title": "Visualization tools for genomic data",
  "Description": "The ggbio package extends and specializes the grammar of\ngraphics for biological data. The graphics are designed to\nanswer common scientific questions, in particular those often\nasked of high throughput genomics data. All core Bioconductor\ndata structures are supported, where appropriate. The package\nsupports detailed views of particular genomic regions, as well\nas genome-wide overviews. Supported overviews include ideograms\nand grand linear views. High-level plots include sequence\nfragment length, edge-linked interval to data view, mismatch\npileup, and several splicing summaries.",
  "Authors@R": "c(person(\"Tengfei\", \"Yin\", role=c(\"aut\"),\nemail=\"yintengfei@gmail.com\"),\nperson(\"Michael\", \"Lawrence\", role=c(\"aut\", \"ths\", \"cre\"),\nemail=\"lawremi@gmail.com\"),\nperson(\"Dianne\", \"Cook\", role=c(\"aut\", \"ths\")),\nperson(\"Sanchit\", \"Saini\", role=\"ctb\"),\nperson(\"Johannes\", \"Rainer\", role=\"ctb\"))",
  "VignetteBuilder": "knitr",
  "URL": "https://lawremi.github.io/ggbio/",
  "BugReports": "https://github.com/lawremi/ggbio/issues",
  "License": "Artistic-2.0",
  "LazyLoad": "Yes",
  "Collate": "AllClasses.R AllGenerics.R Cache-class.R GGbio-class.R\nGrob-class.R ideogram.R Tracked-class.R Plot-class.R\nggplot-method.R theme.R Tracks-class.R geom_chevron-method.R\ngeom_alignment-method.R geom_arch-method.R geom_arrow-method.R\ngeom_arrowrect-method.R geom_rect-method.R\ngeom_segment-method.R geom_bar-method.R layout_circle-method.R\nlayout_karyogram-method.R layout_linear-method.R\nstat_aggregate-method.R stat_coverage-method.R\nstat_identity-method.R stat_mismatch-method.R\nstat_stepping-method.R stat_gene-method.R stat_table-method.R\nstat_bin-method.R stat_slice-method.R stat_reduce-method.R\ncoord_genome-method.R autoplot-method.R hack.R\nplotGrandLinear.R plotRangesLinkedToData.R\nplotFragLength-method.R plotSpliceSum-method.R rescale-method.R\nscales.R utils.R zzz.R",
  "biocViews": "Infrastructure, Visualization",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:36:00 UTC",
  "RemoteUrl": "https://github.com/bioc/ggbio",
  "RemoteRef": "HEAD",
  "RemoteSha": "5d6ed36bdeb6e37a8743bd3e03cfe3637dd227a9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:32:08 UTC",
    "User": "root"
  },
  "Author": "Tengfei Yin [aut],\nMichael Lawrence [aut, ths, cre],\nDianne Cook [aut, ths],\nSanchit Saini [ctb],\nJohannes Rainer [ctb]",
  "Maintainer": "Michael Lawrence <lawremi@gmail.com>",
  "MD5sum": "ed9b24ab01ae8e226b9be637cb06240b",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-30T08:32:08.000Z",
  "_published": "2026-05-30T12:11:16.634Z",
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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    "extra/contents.json",
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  "_homeurl": "https://github.com/lawremi/ggbio",
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  "_exports": [
    "align.plots",
    "alignPlots",
    "arrangeGrobByParsingLegend",
    "autoplot",
    "backup",
    "bgColor",
    "bgColor<-",
    "cbind",
    "circle",
    "fixed",
    "fixed<-",
    "geom_alignment",
    "geom_arch",
    "geom_arrow",
    "geom_arrowrect",
    "geom_bar",
    "geom_chevron",
    "geom_rect",
    "geom_segment",
    "ggbio",
    "GGbio",
    "ggsave",
    "hasAxis",
    "hasAxis<-",
    "height",
    "height<-",
    "Ideogram",
    "labeled",
    "labeled<-",
    "layout_circle",
    "layout_karyogram",
    "mutable",
    "mutable<-",
    "nextView",
    "plotFragLength",
    "plotGrandLinear",
    "plotIdeogram",
    "plotKaryogram",
    "plotRangesLinkedToData",
    "plotSpliceSum",
    "plotStackedOverview",
    "prevView",
    "rbind",
    "rescale",
    "reset",
    "scale_fill_fold_change",
    "scale_fill_giemsa",
    "scale_x_sequnit",
    "stat_aggregate",
    "stat_bin",
    "stat_coverage",
    "stat_gene",
    "stat_identity",
    "stat_mismatch",
    "stat_reduce",
    "stat_slice",
    "stat_stepping",
    "stat_table",
    "theme_alignment",
    "theme_clear",
    "theme_genome",
    "theme_noexpand",
    "theme_null",
    "theme_pack_panels",
    "theme_tracks_sunset",
    "tracks",
    "xlim",
    "xlim<-",
    "zoom",
    "zoom_in",
    "zoom_out"
  ],
  "_help": [
    {
      "page": "arrangeGrobByParsingLegend",
      "title": "Arrange grobs by parse their legend.",
      "topics": [
        "arrangeGrobByParsingLegend"
      ]
    },
    {
      "page": "autoplot-method",
      "title": "Generic autoplot function",
      "topics": [
        "+,Bioplot,Any-method",
        "autoplot",
        "autoplot,BamFile-method",
        "autoplot,BamFileList-method",
        "autoplot,BSgenome-method",
        "autoplot,character-method",
        "autoplot,ExpressionSet-method",
        "autoplot,GAlignments-method",
        "autoplot,GRanges-method",
        "autoplot,GRangesList-method",
        "autoplot,IRanges-method",
        "autoplot,matrix-method",
        "autoplot,OrganismDb-method",
        "autoplot,RangedSummarizedExperiment-method",
        "autoplot,Rle-method",
        "autoplot,RleList-method",
        "autoplot,Seqinfo-method",
        "autoplot,TabixFile-method",
        "autoplot,TxDbOREnsDb-method",
        "autoplot,VCF-method",
        "autoplot,Views-method",
        "autoplot,VRanges-method"
      ]
    },
    {
      "page": "geom_alignment-method",
      "title": "Alignment geoms for GRanges object",
      "topics": [
        "geom_alignment",
        "geom_alignment,BamFile-method",
        "geom_alignment,GRanges-method",
        "geom_alignment,GRangesList-method",
        "geom_alignment,missing-method",
        "geom_alignment,OrganismDb-method",
        "geom_alignment,TxDbOREnsDb-method",
        "geom_alignment,uneval-method"
      ]
    },
    {
      "page": "geom_arch-method",
      "title": "Arch geoms for GRanges object",
      "topics": [
        "geom_arch",
        "geom_arch,data.frame-method",
        "geom_arch,GRanges-method",
        "geom_arch,missing-method",
        "geom_arch,uneval-method"
      ]
    },
    {
      "page": "geom_arrow-method",
      "title": "Arrow geoms for GRanges object",
      "topics": [
        "geom_arrow",
        "geom_arrow,GRanges-method",
        "geom_arrow,missing-method",
        "geom_arrow,uneval-method"
      ]
    },
    {
      "page": "geom_arrowrect-method",
      "title": "Arrowrect geoms for GRanges object",
      "topics": [
        "geom_arrowrect",
        "geom_arrowrect,GRanges-method",
        "geom_arrowrect,missing-method",
        "geom_arrowrect,uneval-method"
      ]
    },
    {
      "page": "geom_bar-method",
      "title": "Segment geoms for GRanges object",
      "topics": [
        "geom_bar",
        "geom_bar,ANY-method",
        "geom_bar,chevron-method",
        "geom_bar,GRanges-method",
        "geom_bar,missing-method"
      ]
    },
    {
      "page": "geom_chevron-method",
      "title": "Chevron geoms for GRanges object",
      "topics": [
        "geom_chevron",
        "geom_chevron,GRanges-method",
        "geom_chevron,missing-method",
        "geom_chevron,uneval-method"
      ]
    },
    {
      "page": "geom_rect-method",
      "title": "Rect geoms for GRanges object",
      "topics": [
        "geom_rect",
        "geom_rect,ANY-method",
        "geom_rect,GRanges-method",
        "geom_rect,missing-method",
        "geom_rect,uneval-method"
      ]
    },
    {
      "page": "geom_segment-method",
      "title": "Segment geoms for GRanges object",
      "topics": [
        "geom_segment",
        "geom_segment,ANY-method",
        "geom_segment,GRanges-method",
        "geom_segment,missing-method",
        "geom_segment,uneval-method"
      ]
    },
    {
      "page": "ggbio-class",
      "title": "class ggbio",
      "topics": [
        "$,GGbio-method",
        "$<-,GGbio-method",
        "+,GGbio,ANY-method",
        "GGbio",
        "ggbio",
        "GGbio-class",
        "ggbio-class"
      ]
    },
    {
      "page": "ggplot-method",
      "title": "ggplot methods",
      "topics": [
        "ggplot.BSgenome",
        "ggplot.character",
        "ggplot.ExpressionSet",
        "ggplot.GAlignments",
        "ggplot.matrix",
        "ggplot.RsamtoolsFile",
        "ggplot.Seqinfo",
        "ggplot.SummarizedExperiment",
        "ggplot.TxDbOREnsDb",
        "ggplot.VCF",
        "ggplot.Vector"
      ]
    },
    {
      "page": "ggsave",
      "title": "Save a ggplot object or tracks with sensible defaults",
      "topics": [
        "ggsave"
      ]
    },
    {
      "page": "Grob-class",
      "title": "Grob getter",
      "topics": [
        "ggplotGrob-class",
        "Grob",
        "Grob,gg-method",
        "Grob,GGbio-method",
        "Grob,gtable-method",
        "Grob,lattice-method",
        "Grob,trellis-method",
        "Grob-class",
        "Grob-method",
        "GrobList",
        "GrobList-class",
        "latticeGrob-class"
      ]
    },
    {
      "page": "plotSingleChrom",
      "title": "Plot single chromosome with cytobands",
      "topics": [
        "+,Ideogram,ANY-method",
        "Ideogram",
        "Ideogram-class",
        "plotIdeogram"
      ]
    },
    {
      "page": "layout_circle-method",
      "title": "Create a circle layout",
      "topics": [
        "circle",
        "layout_circle",
        "layout_circle,GRanges-method",
        "layout_circle,missing-method",
        "layout_circle,uneval-method"
      ]
    },
    {
      "page": "layout_karyogram-method",
      "title": "Create a karyogram layout",
      "topics": [
        "layout_karyogram",
        "layout_karyogram,GRanges-method"
      ]
    },
    {
      "page": "Plot-class",
      "title": "Plot class",
      "topics": [
        "ggbioPlot-class",
        "ggplotPlot-class",
        "latticePlot-class",
        "Plot",
        "Plot,gg-method",
        "Plot,GGbio-method",
        "Plot,Ideogram-method",
        "Plot,trellis-method",
        "Plot-class"
      ]
    },
    {
      "page": "plotFragLength",
      "title": "Plot estimated fragment length for paired-end RNA-seq data",
      "topics": [
        "plotFragLength",
        "plotFragLength,character,GRanges-method"
      ]
    },
    {
      "page": "plotGrandLinear",
      "title": "Manhattan for GWAS",
      "topics": [
        "plotGrandLinear"
      ]
    },
    {
      "page": "plotRangesLinkedToData",
      "title": "Plot Ranges Linked with Data",
      "topics": [
        "plotRangesLinkedToData",
        "plotRangesLinkedToData,GenomicRanges_OR_GRangesList-method",
        "plotRangesLinkedToData,RangedSummarizedExperiment-method"
      ]
    },
    {
      "page": "plotSpliceSum",
      "title": "Plot Splice Summary from RNA-seq data",
      "topics": [
        "plotSpliceSum",
        "plotSpliceSum,character,EnsDb-method",
        "plotSpliceSum,character,GRangesList-method",
        "plotSpliceSum,character,TxDb-method"
      ]
    },
    {
      "page": "plotStackedOverview",
      "title": "Plot stacked overview",
      "topics": [
        "plotKaryogram",
        "plotStackedOverview"
      ]
    },
    {
      "page": "rescale-method",
      "title": "rescale ggplot object",
      "topics": [
        "rescale",
        "rescale,gg-method",
        "rescale,ggplot-method",
        "rescale,numeric-method"
      ]
    },
    {
      "page": "scale_fill_fold_change",
      "title": "scale color for fold change values",
      "topics": [
        "scale_fill_fold_change"
      ]
    },
    {
      "page": "scale_fill_giemsa",
      "title": "scale filled color to customized giemsa color.",
      "topics": [
        "scale_fill_giemsa"
      ]
    },
    {
      "page": "scale_x_sequnit",
      "title": "scale x by unit",
      "topics": [
        "scale_x_sequnit"
      ]
    },
    {
      "page": "stat_aggregate-method",
      "title": "Generates summaries on the specified windows",
      "topics": [
        "stat_aggregate",
        "stat_aggregate,GRanges-method",
        "stat_aggregate,missing-method",
        "stat_aggregate,uneval-method"
      ]
    },
    {
      "page": "stat_bin-method",
      "title": "Binning method",
      "topics": [
        "stat_bin",
        "stat_bin,ANY-method",
        "stat_bin,missing-method",
        "stat_bin,Rle-method",
        "stat_bin,RleList-method",
        "stat_bin,uneval-method"
      ]
    },
    {
      "page": "stat_coverage-method",
      "title": "Calculate coverage",
      "topics": [
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        "stat_coverage,BamFile-method",
        "stat_coverage,GRanges-method",
        "stat_coverage,GRangesList-method",
        "stat_coverage,missing-method",
        "stat_coverage,uneval-method"
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    },
    {
      "page": "stat_gene-method",
      "title": "Calculate gene structure",
      "topics": [
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        "stat_gene,TxDb-method"
      ]
    },
    {
      "page": "stat_identity-method",
      "title": "Transform the data to a data.frame and for multiple geoms.",
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        "stat_identity,ANY-method",
        "stat_identity,GRanges-method",
        "stat_identity,missing-method",
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        "stat_identity,RleList-method",
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    },
    {
      "page": "stat_mismatch-method",
      "title": "Calculate mismatch summary",
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        "stat_mismatch,GRanges-method",
        "stat_mismatch,missing-method",
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    {
      "page": "stat_reduce-method",
      "title": "Reduce an object.",
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        "stat_reduce,GRanges-method",
        "stat_reduce,IRanges-method",
        "stat_reduce,missing-method",
        "stat_reduce,TxDbOREnsDb-method",
        "stat_reduce,uneval-method"
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      "page": "stat_slice-method",
      "title": "Slice Rle/RleList to view them as bar or heatmap.",
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        "stat_slice,Rle-method",
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      "page": "stat_stepping-method",
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    },
    {
      "page": "theme",
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        "theme_noexpand",
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    },
    {
      "page": "Tracked-class",
      "title": "Tracked class",
      "topics": [
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        "Tracked-class"
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    },
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        "+,Tracks,position_c-method",
        "+,Tracks,theme-method",
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    {
      "page": "nav",
      "title": "Simple navigation for ggbio object.",
      "topics": [
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      "title": "Part 0: Introduction and quick start",
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      "headings": [],
      "created": "2013-11-01 20:21:51",
      "modified": "2013-11-01 20:21:51",
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