{ "_id": "6a1acfac1d7bb097a09e0c3a", "Package": "Gviz", "Title": "Plotting data and annotation information along genomic\ncoordinates", "Version": "1.57.0", "Authors@R": "c(person(\"Florian\", \"Hahne\", role=\"aut\"),\nperson(\"Steffen\", \"Durinck\", role=\"aut\"),\nperson(\"Robert\", \"Ivanek\", role=c(\"aut\", \"cre\"),\nemail=\"robert.ivanek@unibas.ch\",\ncomment=c(ORCID=\"0000-0002-8403-056X\")),\nperson(\"Arne\", \"Mueller\", role=\"aut\"),\nperson(\"Steve\", \"Lianoglou\", role=\"aut\"),\nperson(\"Ge\", \"Tan\", role=\"aut\"),\nperson(\"Lance\", \"Parsons\", role=\"aut\"),\nperson(\"Shraddha\", \"Pai\", role=\"aut\"),\nperson(\"Thomas\", \"McCarthy\", role=\"ctb\"),\nperson(\"Felix\", \"Ernst\", role=\"ctb\"),\nperson(\"Mike\", \"Smith\", role=\"ctb\"))", "Description": "Genomic data analyses requires integrated visualization of\nknown genomic information and new experimental data. Gviz uses\nthe biomaRt and the rtracklayer packages to perform live\nannotation queries to Ensembl and UCSC and translates this to\ne.g. gene/transcript structures in viewports of the grid\ngraphics package. This results in genomic information plotted\ntogether with your data.", "LazyLoad": "yes", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "biocViews": "Visualization, Microarray, Sequencing", "URL": "https://github.com/ivanek/Gviz", "BugReports": "https://github.com/ivanek/Gviz/issues", "VignetteBuilder": "knitr", "License": "Artistic-2.0", "Collate": "'utils.R' 'ImageMap-class.R' 'DisplayPars-class.R'\n'GdObject-class.R' 'ReferenceTrack-class.R'\n'SequenceTrack-class.R' 'RangeTrack-class.R'\n'StackedTrack-class.R' 'NumericTrack-class.R'\n'DataTrack-class.R' 'AlignmentsTrack-class.R'\n'AnnotationTrack-class.R' 'GeneRegionTrack-class.R'\n'BiomartGeneRegionTrack-class.R' 'CustomTrack-class.R'\n'GenomeAxisTrack-class.R' 'Gviz-defunct.R' 'Gviz-deprecated.R'\n'HighlightTrack-class.R' 'IdeogramTrack-class.R'\n'OverlayTrack-class.R' 'UcscTrack.R' 'collapsing.R'\n'datasets.R' 'exportTracks.R' 'grouping.R' 'plotTracks.R'\n'settings.R'", "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 12:36:16 UTC", "RemoteUrl": "https://github.com/bioc/Gviz", "RemoteRef": "HEAD", "RemoteSha": "03023417368100d20ca70792450d54de719f3dff", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:12:58 UTC", "User": "root" }, "Author": "Florian Hahne [aut],\nSteffen Durinck [aut],\nRobert Ivanek [aut, cre] (ORCID:\n),\nArne Mueller [aut],\nSteve Lianoglou [aut],\nGe Tan [aut],\nLance Parsons [aut],\nShraddha Pai [aut],\nThomas McCarthy [ctb],\nFelix Ernst [ctb],\nMike Smith [ctb]", "Maintainer": "Robert Ivanek ", "MD5sum": "886ac38dd50c198ed489d9481c0424d5", "_user": "bioc", "_type": "src", "_file": "Gviz_1.57.0.tar.gz", "_fileid": "91d6e2f7dd33c8ea62290c6343f6ece65c73132d3b3360617c301e088ac6653f", "_filesize": 7761443, "_sha256": "91d6e2f7dd33c8ea62290c6343f6ece65c73132d3b3360617c301e088ac6653f", "_created": "2026-05-30T08:12:58.000Z", "_published": "2026-05-30T11:53:16.900Z", "_jobs": [ { "job": 78635866452, "time": 305, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306774437" }, { "job": 78635866465, "time": 634, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306806467" }, { "job": 78635866460, "time": 649, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306807911" }, { "job": 78635866448, "time": 312, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307965738" }, { "job": 78635866447, "time": 451, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307977414" }, { "job": 78635464674, "time": 473, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306745445" }, { "job": 78635866449, "time": 229, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306767444" }, { "job": 78635866463, "time": 582, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306801599" }, { "job": 78635866466, "time": 582, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306801720" }, { "job": 78635866462, "time": 526, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306795996" } ], "_bioccheck": { "error": 0, "warning": 3, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678812440", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Gviz", "_commit": { "id": "03023417368100d20ca70792450d54de719f3dff", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379776 }, "_maintainer": { "name": "Robert Ivanek", "email": "robert.ivanek@unibas.ch", "login": "ivanek", "description": "", "uuid": 646540, "orcid": "0000-0002-8403-056X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "S4Vectors", "version": ">= 0.9.25", "role": "Depends" }, { "package": "IRanges", "version": ">= 1.99.18", "role": "Depends" }, { "package": "GenomicRanges", "version": ">= 1.61.1", "role": "Depends" }, { "package": "grid", "role": "Depends" }, { "package": "XVector", "version": ">= 0.5.7", "role": "Imports" }, { "package": "rtracklayer", "version": ">= 1.69.1", "role": "Imports" }, { "package": "lattice", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "biomaRt", "version": ">= 2.11.0", "role": "Imports" }, { "package": "AnnotationDbi", "version": ">= 1.27.5", "role": "Imports" }, { "package": "Biobase", "version": ">= 2.15.3", "role": "Imports" }, { "package": "GenomicFeatures", "version": ">= 1.61.4", "role": "Imports" }, { "package": "ensembldb", "version": ">= 2.11.3", "role": "Imports" }, { "package": "BSgenome", "version": ">= 1.77.1", "role": "Imports" }, { "package": "Biostrings", "version": ">= 2.77.2", "role": "Imports" }, { "package": "biovizBase", "version": ">= 1.13.8", "role": "Imports" }, { "package": "Rsamtools", "version": ">= 2.25.1", "role": "Imports" }, { "package": "latticeExtra", "version": ">= 0.6-26", "role": "Imports" }, { "package": "matrixStats", "version": ">= 0.8.14", "role": "Imports" }, { "package": "GenomicAlignments", "version": ">= 1.45.1", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "BiocGenerics", "version": ">= 0.11.3", "role": "Imports" }, { "package": "digest", "version": ">= 0.6.8", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" }, { "package": "xml2", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 49, "_updates": [ { "week": "2025-25", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.57.0", "bioc": "3.24" }, { "branch": "release", "version": "1.56.0", "bioc": "3.23" } ], "_topics": [ "visualization", "microarray", "sequencing" ], "_stars": 92, "_contributors": [ { "user": "ivanek", "count": 241, "uuid": 646540 }, { "user": "dtenenba", "count": 23, "uuid": 2286826 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 10, "uuid": 1744257 }, { "user": "felixernst", "count": 6, "uuid": 17824332 }, { "user": "lparsons", "count": 3, "uuid": 645128 }, { "user": "hpages", "count": 3, "uuid": 8810451 }, { "user": "muellar2", "count": 2, "uuid": 87768373 }, { "user": "grimbough", "count": 2, "uuid": 971237 }, { "user": "twmccart", "count": 2, "uuid": 10548984 }, { "user": "vjcitn", "count": 2, "uuid": 4624066 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "lianos", "count": 1, "uuid": 25496 }, { "user": "aoles", "count": 1, "uuid": 6545356 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 6145, "source": "https://www.bioconductor.org/packages/stats/bioc/Gviz" }, "_mentions": 134, "_devurl": "https://github.com/ivanek/gviz", "_searchresults": 2000, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/Gviz.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ivanek/gviz", "_realowner": "bioc", "_cranurl": false, "_exports": [ ".chrName", ".DisplayPars", ".doCache", "addScheme", "AlignmentsTrack", "AnnotationTrack", "as.list", "availableDefaultMapping", "availableDisplayPars", "BiomartGeneRegionTrack", "chromosome", "chromosome<-", "clearSessionCache", "consolidateTrack", "coords", "CustomTrack", "DataTrack", "DetailsAnnotationTrack", "displayPars", "DisplayPars", "displayPars<-", "drawAxis", "drawGD", "end", "end<-", "exon", "exon<-", "exportTracks", "feature", "feature<-", "gene", "gene<-", "GeneRegionTrack", "genome", "genome<-", "GenomeAxisTrack", "getPar", "getScheme", "group", "group<-", "HighlightTrack", "identifier", "identifier<-", "IdeogramTrack", "imageMap", "imageMap<-", "initialize", "OverlayTrack", "plotTracks", "position", "RNASequenceTrack", "seqinfo", "seqlevels", "seqnames", "SequenceTrack", "setCoverage", "setPar", "setStacks", "show", "split", "stacking", "stacking<-", "stacks", "start", "start<-", "strand", "strand<-", "subset", "symbol", "symbol<-", "tags", "transcript", "transcript<-", "UcscTrack", "values", "values<-", "width", "width<-" ], "_datasets": [ { "name": "axTrack", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "GenomeAxisTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "biomTrack", "title": "Data sets", "object": "biomTrack", "file": "biomTrack.rda", "class": [ "BiomartGeneRegionTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "biomTrack2", "title": "Data sets", "object": "biomTrack2", "file": "biomTrack2.rda", "class": [ "BiomartGeneRegionTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "bmt", "title": "Data sets", "object": "alTrackGenes", "file": "alTrackGenes.rda", "class": [ "BiomartGeneRegionTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "bmTrack", "title": "Data sets", "object": "bmTrack", "file": "bmTrack.rda", "class": [ "BiomartGeneRegionTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "conservation", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "DataTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "cpgIslands", "title": "Data sets", "object": "cpgIslands", "file": "cpgIslands.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "cpgIslands", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "AnnotationTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "ctrack", "title": "Data sets", "object": "collapseTrack", "file": "collapseTrack.rda", "class": [ "AnnotationTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "cyp2b10", "title": "Data sets", "object": "cyp2b10", "file": "cyp2b10.rda", "class": [ "data.frame" ], "fields": [ "chromosome", "start", "end", "width", "strand", "feature", "gene", "exon", "transcript", "symbol" ], "rows": 25, "table": true, "tojson": true }, { "name": "denseAnnTrack", "title": "Data sets", "object": "denseAnnTrack", "file": "denseAnnTrack.rda", "class": [ "AnnotationTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "dtHoriz", "title": "Data sets", "object": "dtHoriz", "file": "dtHoriz.rda", "class": [ "DataTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "ensGenes", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "GeneRegionTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "from", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "gcContent", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "DataTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "geneDetails", "title": "Data sets", "object": "geneDetails", "file": "geneDetails.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "geneModels", "title": "Data sets", "object": "geneModels", "file": "geneModels.rda", "class": [ "data.frame" ], "fields": [ "chromosome", "start", "end", "width", "strand", "feature", "gene", "exon", "transcript", "symbol" ], "rows": 97, "table": true, "tojson": true }, { "name": "ideoTrack", "title": "Data sets", "object": "ideoTrack", "file": "ideoTrack.rda", "class": [ "IdeogramTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "idTrack", "title": "Data sets", "object": "idTrack", "file": "idTrack.rda", "class": [ "IdeogramTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "idxTrack", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "IdeogramTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "itrack", "title": "Data sets", "object": "itrack", "file": "itrack.rda", "class": [ "IdeogramTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "knownGenes", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "GeneRegionTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "refGenes", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "GeneRegionTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "snpLocations", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "AnnotationTrack" ], "fields": [], "table": false, "tojson": false }, { "name": "to", "title": "Data sets", "object": "ucscItems", "file": "ucscItems.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "twoGroups", "title": "Data sets", "object": "twoGroups", "file": "twoGroups.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "AlignmentsTrack-class", "title": "AlignmentsTrack class and methods", "topics": [ "AlignmentsTrack", "AlignmentsTrack-class", "chromosome<-,AlignmentsTrack-method", "drawAxis,AlignmentsTrack-method", "drawGD,AlignmentsTrack-method", "initialize,AlignmentsTrack-method", "initialize,ReferenceAlignmentsTrack-method", "ReferenceAlignmentsTrack-class", "setStacks,AlignmentsTrack-method", "show,AlignmentsTrack-method", "show,ReferenceAlignmentsTrack-method", "stacks,AlignmentsTrack-method", "subset,AlignmentsTrack-method", "subset,ReferenceAlignmentsTrack-method", "values,AlignmentsTrack-method" ] }, { "page": "ReferenceTrack-class", "title": "ReferenceTrack class and methods", "topics": [ "availableDefaultMapping", "initialize,ReferenceTrack-method", "ReferenceTrack-class" ] }, { "page": "BiomartGeneRegionTrack-class", "title": "BiomartGeneRegionTrack class and methods", "topics": [ "BiomartGeneRegionTrack", "BiomartGeneRegionTrack-class", "initialize,BiomartGeneRegionTrack-method", "subset,BiomartGeneRegionTrack-method" ] }, { "page": "collapsing", "title": "Dynamic content based on the available resolution", "topics": [ "collapsing" ] }, { "page": "CustomTrack-class", "title": "CustomTrack class and methods", "topics": [ "CustomTrack", "CustomTrack-class", "drawGD,CustomTrack-method", "initialize,CustomTrack-method", "show,CustomTrack-method" ] }, { "page": "datasets", "title": "Data sets", "topics": [ "axTrack", "biomTrack", "biomTrack2", "bmt", "bmTrack", "conservation", "cpgIslands", "ctrack", "cyp2b10", "datasets", "denseAnnTrack", "dtHoriz", "ensGenes", "from", "gcContent", "geneDetails", "geneModels", "ideoTrack", "idTrack", "idxTrack", "iTrack", "itrack", "knownGenes", "refGenes", "snpLocations", "to", "twoGroups" ] }, { "page": "DisplayPars-class", "title": "DisplayPars: A class to control the plotting parameters for GdObjects", "topics": [ ".DisplayPars", "as.list,DisplayPars-method", "as.list,InferredDisplayPars-method", "availableDisplayPars", "DisplayPars", "displayPars", "displayPars,DisplayPars,character-method", "displayPars,DisplayPars,missing-method", "DisplayPars-class", "displayPars<-", "displayPars<-,DisplayPars,list-method", "getPar", "getPar,DisplayPars,character-method", "getPar,DisplayPars,missing-method", "setPar", "setPar,DisplayPars,character-method", "setPar,DisplayPars,list-method", "show,DisplayPars-method", "show,InferredDisplayPars-method" ] }, { "page": "exportTracks", "title": "Export Gviz tracks into an annotation file representation.", "topics": [ "exportTracks" ] }, { "page": "GeneRegionTrack-class", "title": "GeneRegionTrack class and methods", "topics": [ "drawGD,GeneRegionTrack-method", "exon,GeneRegionTrack-method", "exon<-,GeneRegionTrack,character-method", "gene,GeneRegionTrack-method", "gene<-,GeneRegionTrack,character-method", "GeneRegionTrack", "GeneRegionTrack-class", "group,GeneRegionTrack-method", "group<-,GeneRegionTrack,character-method", "identifier,GeneRegionTrack-method", "identifier<-,GeneRegionTrack,character-method", "initialize,GeneRegionTrack-method", "initialize,ReferenceGeneRegionTrack-method", "ReferenceGeneRegionTrack-class", "show,GeneRegionTrack-method", "show,ReferenceGeneRegionTrack-method", "subset,ReferenceGeneRegionTrack-method", "symbol,GeneRegionTrack-method", "symbol<-,GeneRegionTrack,character-method", "transcript,GeneRegionTrack-method", "transcript<-,GeneRegionTrack,character-method" ] }, { "page": "grouping", "title": "Grouping of annotation features", "topics": [ "grouping" ] }, { "page": "Gviz-defunct", "title": "Defunct functions in package 'Gviz'", "topics": [ "Gviz-defunct" ] }, { "page": "Gviz-deprecated", "title": "Deprecated functions in package 'Gviz'", "topics": [ "Gviz-deprecated" ] }, { "page": "HighlightTrack-class", "title": "HighlightTrack class and methods", "topics": [ "chromosome<-,HighlightTrack-method", "consolidateTrack,HighlightTrack-method", "displayPars<-,HighlightTrack,list-method", "HighlightTrack", "HighlightTrack-class", "initialize,HighlightTrack-method", "length,HighlightTrack-method", "setStacks,HighlightTrack-method", "show,HighlightTrack-method", "subset,HighlightTrack-method" ] }, { "page": "IdeogramTrack-class", "title": "IdeogramTrack class and methods", "topics": [ "chromosome<-,IdeogramTrack-method", "drawGD,IdeogramTrack-method", "end,IdeogramTrack-method", "end<-,IdeogramTrack-method", "genome<-,IdeogramTrack-method", "IdeogramTrack", "IdeogramTrack-class", "initialize,IdeogramTrack-method", "length,IdeogramTrack-method", "position,IdeogramTrack-method", "show,IdeogramTrack-method", "start,IdeogramTrack-method", "start<-,IdeogramTrack-method", "subset,IdeogramTrack-method", "width,IdeogramTrack-method", "width<-,IdeogramTrack-method", "[,IdeogramTrack,ANY,ANY,ANY-method", "[,IdeogramTrack,ANY,ANY-method", "[,IdeogramTrack-method" ] }, { "page": "NumericTrack-class", "title": "NumericTrack class and methods", "topics": [ "drawAxis,NumericTrack-method", "drawGrid,NumericTrack-method", "NumericTrack-class" ] }, { "page": "plotTracks", "title": "The main plotting function for one or several Gviz tracks.", "topics": [ "plotTracks" ] }, { "page": "RangeTrack-class", "title": "RangeTrack class and methods", "topics": [ "chromosome,RangeTrack-method", "chromosome<-,RangeTrack-method", "consolidateTrack,RangeTrack-method", "end,RangeTrack-method", "end<-,RangeTrack-method", "feature,RangeTrack-method", "feature<-,RangeTrack,character-method", "genome,RangeTrack-method", "genome<-,RangeTrack-method", "initialize,RangeTrack-method", "length,RangeTrack-method", "max,RangeTrack-method", "min,RangeTrack-method", "position,RangeTrack-method", "range,RangeTrack-method", "ranges,RangeTrack-method", "RangeTrack-class", "seqinfo,RangeTrack-method", "seqlevels,RangeTrack-method", "seqnames,RangeTrack-method", "split,RangeTrack,ANY-method", "start,RangeTrack-method", "start<-,RangeTrack-method", "strand,RangeTrack-method", "strand<-,RangeTrack,ANY-method", "subset,RangeTrack-method", "values,RangeTrack-method", "width,RangeTrack-method", "width<-,RangeTrack-method", "[,RangeTrack,ANY,ANY,ANY-method" ] }, { "page": "SequenceTrack-class", "title": "SequenceTrack class and methods", "topics": [ "chromosome,SequenceTrack-method", "chromosome<-,SequenceTrack-method", "consolidateTrack,SequenceTrack-method", "drawGD,SequenceTrack-method", "end,SequenceTrack-method", "genome,SequenceTrack-method", "initialize,ReferenceSequenceTrack-method", "initialize,SequenceBSgenomeTrack-method", "initialize,SequenceDNAStringSetTrack-method", "initialize,SequenceRNAStringSetTrack-method", "initialize,SequenceTrack-method", "length,SequenceTrack-method", "ReferenceSequenceTrack-class", "RNASequenceTrack", "seqlevels,SequenceBSgenomeTrack-method", "seqlevels,SequenceTrack-method", "seqnames,SequenceBSgenomeTrack-method", "seqnames,SequenceTrack-method", "SequenceBSgenomeTrack-class", "SequenceDNAStringSetTrack-class", "SequenceRNAStringSetTrack-class", "SequenceTrack", "SequenceTrack-class", "show,ReferenceSequenceTrack-method", "show,SequenceBSgenomeTrack-method", "show,SequenceDNAStringSetTrack-method", "show,SequenceRNAStringSetTrack-method", "start,SequenceTrack-method", "width,SequenceTrack-method" ] }, { "page": "settings", "title": "Setting display parameters to control the look and feel of the plots", "topics": [ "addScheme", "getScheme", "settings" ] }, { "page": "StackedTrack-class", "title": "StackedTrack class and methods", "topics": [ "consolidateTrack,StackedTrack-method", "drawGD,StackedTrack-method", "initialize,StackedTrack-method", "setStacks,StackedTrack-method", "StackedTrack-class", "stacking,StackedTrack-method", "stacking<-,StackedTrack,character-method", "stacks,StackedTrack-method", "subset,StackedTrack-method", "[,StackedTrack,ANY,ANY,ANY-method" ] }, { "page": "UcscTrack", "title": "Meta-constructor for Gviz tracks fetched directly from the various UCSC data sources.", "topics": [ "clearSessionCache", "UcscTrack" ] } ], "_readme": "https://github.com/bioc/Gviz/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "biovizBase", "bit", "bit64", "bitops", "blob", "BSgenome", "bslib", "cachem", "checkmate", "cigarillo", "cli", "cluster", "codetools", "colorspace", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "deldir", "dichromat", "digest", "dplyr", "ensembldb", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httr", "httr2", "interp", "IRanges", "isoband", "jpeg", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "lattice", "latticeExtra", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "nnet", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "ProtGenerics", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "rpart", "Rsamtools", "RSQLite", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "UCSC.utils", "utf8", "VariantAnnotation", "vctrs", "viridisLite", "withr", "xfun", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "Gviz.Rmd", "filename": "Gviz.html", "title": "The Gviz User Guide", "author": "Florian Hahne, Robert Ivánek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Basic Features", "Plotting parameters", "Setting parameters", "Schemes", "Plotting direction", "Track classes", "GenomeAxisTrack", "Display parameters for GenomeAxisTrack objects", "IdeogramTrack", "Display parameters for IdeogramTrack objects", "DataTrack", "Data Grouping", "Building DataTrack objects from files", "Data transformations", "Display parameters for DataTrack objects", "AnnotationTrack", "Collapsing", "Building AnnotationTrack objects from files", "Display parameters for AnnotationTrack objects", "GeneRegionTrack", "Building GeneRegionTrack objects from TxDbs", "Building GeneRegionTrack objects from EnsDbs", "Display parameters for GeneRegionTrack objects", "BiomartGeneRegionTrack", "Display parameters for BiomartGeneRegionTrack objects", "DetailsAnnotationTrack", "Display parameters for DetailsAnnotationTrack objects", "SequenceTrack", "Display parameters for SequenceTrack objects", "AlignmentsTrack", "Display parameters for AlignmentsTrack objects", "Creating tracks from UCSC data", "Track highlighting and overlays", "Highlighting", "Display parameters for HighlightTrack objects", "Overlays", "Composite plots for multiple chromosomes", "Bioconductor integration and file support", "SessionInfo", "References" ], "created": "2018-12-10 23:49:05", "modified": "2023-11-16 14:37:00", "commits": 26 } ], "_score": 13.510691656342704, "_indexed": true, "_nocasepkg": "gviz", "_universes": [ "bioc", "ivanek" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.57.0", "date": "2026-05-30T08:18:33.000Z", "distro": "noble", "commit": "03023417368100d20ca70792450d54de719f3dff", "fileid": "5b2eefb03ce6ec0b4b2cc607f4eb6612c7d179dc849f6ba185e4e780e8a84041", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678812440" }, { "r": "4.6.0", "os": "linux", "version": "1.57.0", "date": "2026-05-30T08:18:37.000Z", "distro": "noble", "commit": "03023417368100d20ca70792450d54de719f3dff", "fileid": "14eccb6863bb065c383fc52b96df67395eeba46453fef079e42132cff3c63d68", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678812440" }, { "r": "4.5.3", "os": "mac", "version": "1.57.0", "date": "2026-05-30T11:47:06.000Z", "commit": "03023417368100d20ca70792450d54de719f3dff", "fileid": "f2fd06e1a5de6508ca4e3c51140bef9070f939b7708cbdad12c9d3a53d976a61", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678812440" }, { "r": "4.6.0", "os": "mac", "version": "1.57.0", "date": "2026-05-30T11:47:34.000Z", "commit": "03023417368100d20ca70792450d54de719f3dff", "fileid": "aee2be49f84e97ad6d801834f9c966104c4c6e156f4c5e6003ccccfa3dad2b67", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678812440" }, { "r": "4.6.0", "os": "wasm", "version": "1.57.0", "date": "2026-05-30T08:17:52.000Z", "commit": "03023417368100d20ca70792450d54de719f3dff", "fileid": "2e2d60568ca7f3cf2e44881fd08d0e53ccd1687cb09afa60a5875985d97a72f1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678812440" }, { "r": "4.7.0", "os": "win", "version": "1.57.0", "date": "2026-05-30T08:17:01.000Z", "commit": "03023417368100d20ca70792450d54de719f3dff", "fileid": "40712b22d72f9ef316e096391571d9d51bfb417a6abf6f44c6d8066354a8800a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678812440" }, { "r": "4.5.3", "os": "win", "version": "1.57.0", "date": "2026-05-30T08:16:53.000Z", "commit": "03023417368100d20ca70792450d54de719f3dff", "fileid": "149d4758a5bd22321ee5a172995affb060eff2ff7f282fa0237eb13a4fe7ef8a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678812440" }, { "r": "4.6.0", "os": "win", "version": "1.57.0", "date": "2026-05-30T08:16:30.000Z", "commit": "03023417368100d20ca70792450d54de719f3dff", "fileid": "33735e077127757243b19670fa00c51107359092bf116d766a78c7b670669985", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678812440" } ] }