{
  "_id": "6a1ad3701d7bb097a09e3983",
  "Package": "GenVisR",
  "Title": "Genomic Visualizations in R",
  "Version": "1.45.0",
  "Authors@R": "c(person(given=\"Zachary\", family=\"Skidmore\", email=\"zlskidmore@gmail.com\",\nrole=c(\"aut\", \"cre\")), person(given=\"Alex\", family=\"Wagner\", role=\"aut\"),\nperson(given=\"Robert\", family=\"Lesurf\", role=\"aut\"), person(given=\"Katie\",\nfamily=\"Campbell\", role=\"aut\"), person(given=\"Jason\", family=\"Kunisaki\",\nemail=\"kunisakijh@gmail.com\", role=\"aut\"), person(given=\"Obi\", family=\"Griffith\",\nemail=\"ogriffit@genome.wustl.edu\", role=\"aut\"), person(given=\"Malachi\", family=\"Griffith\",\nemail=\"mgriffit@genome.wustl.edu\", role=\"aut\"))",
  "Maintainer": "Zachary Skidmore <zlskidmore@gmail.com>",
  "Description": "Produce highly customizable publication quality graphics\nfor genomic data primarily at the cohort level.",
  "License": "GPL-3 + file LICENSE",
  "BugReports": "https://github.com/griffithlab/GenVisR/issues",
  "biocViews": "Infrastructure, DataRepresentation, Classification, DNASeq",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "NeedsCompilation": "no",
  "Author": "Zachary Skidmore [aut, cre], Alex Wagner [aut], Robert Lesurf\n[aut], Katie Campbell [aut], Jason Kunisaki [aut], Obi Griffith\n[aut], Malachi Griffith [aut]",
  "Collate": "'AllGenerics.R' 'Clinical-class.R' 'GMS_Virtual-class.R'\n'GMS-class.R' 'GMS_v4-class.R' 'GenVisR.R' 'Lolliplot-class.R'\n'MutSpectra-class.R' 'MutationAnnotationFormat_Virtual-class.R'\n'MutationAnnotationFormat-class.R'\n'MutationAnnotationFormat_v1.0-class.R'\n'MutationAnnotationFormat_v2.0-class.R'\n'MutationAnnotationFormat_v2.1-class.R'\n'MutationAnnotationFormat_v2.2-class.R'\n'MutationAnnotationFormat_v2.3-class.R'\n'MutationAnnotationFormat_v2.4-class.R' 'Rainfall-class.R'\n'VEP_Virtual-class.R' 'VEP-class.R' 'VEP_v88-class.R'\n'Waterfall-class.R' 'cnFreq.R' 'cnFreq_buildMain.R'\n'cnFreq_disjoin.R' 'cnFreq_qual.R' 'cnSpec.R'\n'cnSpec_buildMain.R' 'cnSpec_qual.R' 'cnView.R'\n'cnView_buildMain.R' 'cnView_qual.R' 'compIdent.R'\n'compIdent_bamRcnt.R' 'compIdent_bamRcnt_qual.R'\n'compIdent_buildMain.R' 'compIdent_format.R' 'covBars.R'\n'covBars_buildMain.R' 'covBars_qual.R' 'deprecated.R'\n'genCov.R' 'genCov_alignPlot.R'\n'genCov_assign_ggplotGrob_height.R'\n'genCov_assign_ggplotGrob_width.R' 'genCov_buildCov.R'\n'genCov_buildTrack.R' 'genCov_extr_ggplotGrob_height.R'\n'genCov_extr_ggplotGrob_width.R' 'genCov_qual.R'\n'genCov_trackViz.R' 'geneViz.R' 'geneViz_Granges2dataframe.R'\n'geneViz_buildGene.R' 'geneViz_calcGC.R'\n'geneViz_cdsFromTXID.R' 'geneViz_extrCDS.R' 'geneViz_extrUTR.R'\n'geneViz_formatUTR.R' 'geneViz_formatcds.R'\n'geneViz_mapCoordSpace.R' 'geneViz_mapCovCoordSpace.R'\n'geneViz_mergeRegions.R' 'geneViz_mergeTypeRegions.R'\n'geneViz_mergeTypes.R' 'ideoView.R' 'ideoView_buildMain.R'\n'ideoView_formatCytobands.R' 'ideoView_qual.R' 'lohSpec.R'\n'lohSpec_buildMain.R' 'lohSpec_fileGlob.R' 'lohSpec_lohCalc.R'\n'lohSpec_qual.R' 'lohSpec_slidingWindow.R' 'lohSpec_stepCalc.R'\n'lohSpec_tileCalc.R' 'lohSpec_tilePosition.R'\n'lohSpec_tileWindow.R' 'lohSpec_windowPosition.R' 'lohView.R'\n'lohView_buildMain.R' 'lohView_qual.R' 'multi_align.R'\n'multi_buildClin.R' 'multi_chrBound.R' 'multi_cytobandRet.R'\n'multi_selectOut.R' 'multi_subsetChr.R'",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:32 UTC",
  "RemoteUrl": "https://github.com/bioc/GenVisR",
  "RemoteRef": "HEAD",
  "RemoteSha": "eb94b6e2107602b25479bb9f1ff22107915dd2e6",
  "Packaged": {
    "Date": "2026-05-30 08:30:35 UTC",
    "User": "root"
  },
  "MD5sum": "cd2158ab9915131216997cddcd393e7d",
  "_user": "bioc",
  "_type": "src",
  "_file": "GenVisR_1.45.0.tar.gz",
  "_fileid": "fd1894fc5597de49a77b7237870c3d7a7633cc67fcbc2f6e624cb50fa9384b68",
  "_filesize": 5200271,
  "_sha256": "fd1894fc5597de49a77b7237870c3d7a7633cc67fcbc2f6e624cb50fa9384b68",
  "_created": "2026-05-30T08:30:35.000Z",
  "_published": "2026-05-30T12:09:20.126Z",
  "_jobs": [
    {
      "job": 78636752377,
      "time": 378,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306882234"
    },
    {
      "job": 78636752376,
      "time": 644,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7306908354"
    },
    {
      "job": 78636752388,
      "time": 632,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306907069"
    },
    {
      "job": 78636752386,
      "time": 397,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7308049909"
    },
    {
      "job": 78636752372,
      "time": 532,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7308060482"
    },
    {
      "job": 78636133215,
      "time": 722,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306845197"
    },
    {
      "job": 78636752371,
      "time": 337,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306878112"
    },
    {
      "job": 78636752380,
      "time": 625,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7306906533"
    },
    {
      "job": 78636752390,
      "time": 583,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7306902100"
    },
    {
      "job": 78636752383,
      "time": 539,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306897428"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679065816",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/GenVisR",
  "_commit": {
    "id": "eb94b6e2107602b25479bb9f1ff22107915dd2e6",
    "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": 1777380152
  },
  "_maintainer": {
    "name": "Zachary Skidmore",
    "email": "zlskidmore@gmail.com",
    "login": "zlskidmore",
    "twitter": "@zlskidmore",
    "description": "Senior Bioinformatician\nWashington University School of Medicine\nDivision of Oncology\nWalter Lab\nGriffith Lab",
    "uuid": 6145692
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "version": ">= 2.45.8",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "DBI",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.25.4",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.1.0",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "version": ">= 2.0.0",
      "role": "Imports"
    },
    {
      "package": "gtable",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "version": ">= 2.7.5",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "version": ">= 1.8.3",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "viridis",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "BSgenome",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "VariantAnnotation",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "RMySQL",
      "role": "Suggests"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "vdiffr",
      "role": "Suggests"
    },
    {
      "package": "formatR",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg38.knownGene",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg38",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-28",
      "n": 1
    },
    {
      "week": "2025-43",
      "n": 4
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-02",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.45.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.44.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "infrastructure",
    "datarepresentation",
    "classification",
    "dnaseq"
  ],
  "_stars": 224,
  "_contributors": [
    {
      "user": "zlskidmore",
      "count": 919,
      "uuid": 6145692
    },
    {
      "user": "ahwagner",
      "count": 70,
      "uuid": 811065
    },
    {
      "user": "alanocallaghan",
      "count": 40,
      "uuid": 10779688
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "obigriffith",
      "count": 8,
      "uuid": 1638042
    },
    {
      "user": "dtenenba",
      "count": 4,
      "uuid": 2286826
    },
    {
      "user": "hpages",
      "count": 4,
      "uuid": 8810451
    },
    {
      "user": "malachig",
      "count": 3,
      "uuid": 856728
    },
    {
      "user": "lbeltrame",
      "count": 2,
      "uuid": 25192
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "gatoravi",
      "count": 1,
      "uuid": 764948
    },
    {
      "user": "cbrueffer",
      "count": 1,
      "uuid": 2705287
    },
    {
      "user": "joegage",
      "count": 1,
      "uuid": 10454330
    },
    {
      "user": "baptiste",
      "count": 1,
      "uuid": 18970
    },
    {
      "user": "mmoisse",
      "count": 1,
      "uuid": 7941646
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 621,
    "source": "https://www.bioconductor.org/packages/stats/bioc/GenVisR"
  },
  "_mentions": 54,
  "_devurl": "https://github.com/griffithlab/genvisr",
  "_searchresults": 87,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GenVisR.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/griffithlab/genvisr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "Clinical",
    "cnFreq",
    "cnSpec",
    "cnView",
    "compIdent",
    "covBars",
    "drawPlot",
    "genCov",
    "geneViz",
    "getData",
    "getDescription",
    "getGrob",
    "getHeader",
    "getMeta",
    "getMutation",
    "getPath",
    "getPosition",
    "getSample",
    "getVersion",
    "GMS",
    "ideoView",
    "lohSpec",
    "lohView",
    "lolliplot",
    "Lolliplot",
    "MutationAnnotationFormat",
    "MutSpectra",
    "Rainfall",
    "TvTi",
    "VEP",
    "waterfall",
    "Waterfall",
    "writeData"
  ],
  "_datasets": [
    {
      "name": "brcaMAF",
      "title": "Truncated BRCA MAF file",
      "object": "brcaMAF",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Hugo_Symbol",
        "Entrez_Gene_Id",
        "Center",
        "NCBI_Build",
        "Chromosome",
        "Start_Position",
        "End_Position",
        "Strand",
        "Variant_Classification",
        "Variant_Type",
        "Reference_Allele",
        "Tumor_Seq_Allele1",
        "Tumor_Seq_Allele2",
        "dbSNP_RS",
        "dbSNP_Val_Status",
        "Tumor_Sample_Barcode",
        "Matched_Norm_Sample_Barcode",
        "Match_Norm_Seq_Allele1",
        "Match_Norm_Seq_Allele2",
        "Tumor_Validation_Allele1",
        "Tumor_Validation_Allele2",
        "Match_Norm_Validation_Allele1",
        "Match_Norm_Validation_Allele2",
        "Verification_Status",
        "Validation_Status",
        "Mutation_Status",
        "Sequencing_Phase",
        "Sequence_Source",
        "Validation_Method",
        "Score",
        "BAM_File",
        "Sequencer",
        "Tumor_Sample_UUID",
        "Matched_Norm_Sample_UUID",
        "chromosome_name_WU",
        "start_WU",
        "stop_WU",
        "reference_WU",
        "variant_WU",
        "type_WU",
        "gene_name_WU",
        "transcript_name_WU",
        "transcript_species_WU",
        "transcript_source_WU",
        "transcript_version_WU",
        "strand_WU",
        "transcript_status_WU",
        "trv_type_WU",
        "c_position_WU",
        "amino_acid_change_WU",
        "ucsc_cons_WU",
        "domain_WU",
        "all_domains_WU",
        "deletion_substructures_WU",
        "transcript_error"
      ],
      "rows": 2773,
      "table": true,
      "tojson": true
    },
    {
      "name": "cytoGeno",
      "title": "Cytogenetic banding dataset",
      "object": "cytoGeno",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chrom",
        "chromStart",
        "chromEnd",
        "name",
        "gieStain",
        "genome"
      ],
      "rows": 2777,
      "table": true,
      "tojson": true
    },
    {
      "name": "HCC1395_Germline",
      "title": "Germline Calls",
      "object": "HCC1395_Germline",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chromosome",
        "position",
        "n_vaf",
        "t_vaf",
        "sample"
      ],
      "rows": 9200,
      "table": true,
      "tojson": true
    },
    {
      "name": "HCC1395_N",
      "title": "Normal BAM",
      "object": "HCC1395_N",
      "class": [
        "data.frame"
      ],
      "fields": [
        "seqnames",
        "pos",
        "strand",
        "nucleotide",
        "count",
        "which_label"
      ],
      "rows": 59,
      "table": true,
      "tojson": true
    },
    {
      "name": "HCC1395_T",
      "title": "Tumor BAM",
      "object": "HCC1395_T",
      "class": [
        "data.frame"
      ],
      "fields": [
        "seqnames",
        "pos",
        "strand",
        "nucleotide",
        "count",
        "which_label"
      ],
      "rows": 52,
      "table": true,
      "tojson": true
    },
    {
      "name": "hg19chr",
      "title": "hg19 chromosome boundaries",
      "object": "hg19chr",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chromosome",
        "start",
        "end"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "LucCNseg",
      "title": "Truncated CN segments",
      "object": "LucCNseg",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chromosome",
        "start",
        "end",
        "probes",
        "segmean",
        "sample"
      ],
      "rows": 3336,
      "table": true,
      "tojson": true
    },
    {
      "name": "PIK3CA",
      "title": "Subset MAF file for PIK3CA gene",
      "object": "PIK3CA",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Hugo_Symbol",
        "Chromosome",
        "Start_Position",
        "End_Position",
        "Variant_Classification",
        "Reference_Allele",
        "Tumor_Seq_Allele2",
        "Tumor_Sample_Barcode",
        "HGVSc",
        "HGVSp",
        "HGVSp_Short",
        "Transcript_ID",
        "Gene",
        "One_Consequence",
        "cDNA_position",
        "CDS_position",
        "Protein_position",
        "Amino_acids",
        "Codons"
      ],
      "rows": 361,
      "table": true,
      "tojson": true
    },
    {
      "name": "SNPloci",
      "title": "Identity snps",
      "object": "SNPloci",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chr",
        "start",
        "end",
        "var",
        "name"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "brcaMAF",
      "title": "Truncated BRCA MAF file",
      "topics": [
        "brcaMAF"
      ]
    },
    {
      "page": "Clinical-class",
      "title": "Class Clinical",
      "topics": [
        "Clinical",
        "Clinical-class"
      ]
    },
    {
      "page": "cnFreq",
      "title": "Construct copy-number frequency plot",
      "topics": [
        "cnFreq"
      ]
    },
    {
      "page": "cnSpec",
      "title": "Construct copy-number cohort plot",
      "topics": [
        "cnSpec"
      ]
    },
    {
      "page": "cnView",
      "title": "Construct copy-number single sample plot",
      "topics": [
        "cnView"
      ]
    },
    {
      "page": "compIdent",
      "title": "Construct identity snp comparison plot",
      "topics": [
        "compIdent"
      ]
    },
    {
      "page": "covBars",
      "title": "Construct an overall coverage cohort plot",
      "topics": [
        "covBars"
      ]
    },
    {
      "page": "cytoGeno",
      "title": "Cytogenetic banding dataset",
      "topics": [
        "cytoGeno"
      ]
    },
    {
      "page": "drawPlot-methods",
      "title": "Method drawPlot",
      "topics": [
        "drawPlot",
        "drawPlot,Clinical-method",
        "drawPlot,Lolliplot-method",
        "drawPlot,MutSpectra-method",
        "drawPlot,Rainfall-method",
        "drawPlot,Waterfall-method"
      ]
    },
    {
      "page": "genCov",
      "title": "Construct a region of interest coverage plot",
      "topics": [
        "genCov"
      ]
    },
    {
      "page": "geneViz",
      "title": "Construct a gene-features plot",
      "topics": [
        "geneViz"
      ]
    },
    {
      "page": "GenVisR",
      "title": "GenVisR",
      "topics": [
        "GenVisR-package",
        "GenVisR"
      ]
    },
    {
      "page": "getData-methods",
      "title": "Method getData",
      "topics": [
        ".getData_Lolliplot",
        ".getData_MutSpectra",
        ".getData_Rainfall",
        ".getData_waterfall",
        "getData",
        "getData,Clinical-method",
        "getData,ClinicalData-method",
        "getData,Lolliplot-method",
        "getData,LolliplotData-method",
        "getData,MutSpectra-method",
        "getData,MutSpectraPrimaryData-method",
        "getData,Rainfall-method",
        "getData,RainfallPrimaryData-method",
        "getData,Waterfall-method",
        "getData,WaterfallData-method"
      ]
    },
    {
      "page": "getDescription-methods",
      "title": "Method getDescription",
      "topics": [
        "getDescription",
        "getDescription,VEP-method",
        "getDescription,VEP_Virtual-method"
      ]
    },
    {
      "page": "getGrob-methods",
      "title": "Method getGrob",
      "topics": [
        "getGrob",
        "getGrob,Lolliplot-method",
        "getGrob,LolliplotPlots-method",
        "getGrob,MutSpectra-method",
        "getGrob,MutSpectraPlots-method",
        "getGrob,Rainfall-method",
        "getGrob,RainfallPlots-method",
        "getGrob,Waterfall-method",
        "getGrob,WaterfallPlots-method"
      ]
    },
    {
      "page": "getHeader-methods",
      "title": "Method getHeader",
      "topics": [
        "getHeader",
        "getHeader,VEP-method",
        "getHeader,VEP_Virtual-method"
      ]
    },
    {
      "page": "getMeta-methods",
      "title": "Method getMeta",
      "topics": [
        "getMeta",
        "getMeta,GMS-method",
        "getMeta,GMS_Virtual-method",
        "getMeta,MutationAnnotationFormat-method",
        "getMeta,MutationAnnotationFormat_Virtual-method",
        "getMeta,VEP-method",
        "getMeta,VEP_Virtual-method"
      ]
    },
    {
      "page": "getMutation-methods",
      "title": "Method getMutation",
      "topics": [
        "getMutation",
        "getMutation,GMS-method",
        "getMutation,GMS_Virtual-method",
        "getMutation,MutationAnnotationFormat-method",
        "getMutation,MutationAnnotationFormat_Virtual-method",
        "getMutation,VEP-method",
        "getMutation,VEP_Virtual-method"
      ]
    },
    {
      "page": "getPath-methods",
      "title": "Method getPath",
      "topics": [
        "getPath",
        "getPath,GMS-method",
        "getPath,MutationAnnotationFormat-method",
        "getPath,VEP-method"
      ]
    },
    {
      "page": "getPosition-methods",
      "title": "Method getPosition",
      "topics": [
        "getPosition",
        "getPosition,GMS-method",
        "getPosition,GMS_Virtual-method",
        "getPosition,MutationAnnotationFormat-method",
        "getPosition,MutationAnnotationFormat_Virtual-method",
        "getPosition,VEP-method",
        "getPosition,VEP_Virtual-method"
      ]
    },
    {
      "page": "getSample-methods",
      "title": "Method getSample",
      "topics": [
        "getSample",
        "getSample,GMS-method",
        "getSample,GMS_Virtual-method",
        "getSample,MutationAnnotationFormat-method",
        "getSample,MutationAnnotationFormat_Virtual-method",
        "getSample,VEP-method",
        "getSample,VEP_Virtual-method"
      ]
    },
    {
      "page": "getVersion-methods",
      "title": "Method getVersion",
      "topics": [
        "getVersion",
        "getVersion,GMS-method",
        "getVersion,MutationAnnotationFormat-method",
        "getVersion,VEP-method"
      ]
    },
    {
      "page": "GMS_v4-class",
      "title": "Class GMS_v4",
      "topics": [
        "GMS_v4",
        "GMS_v4-class"
      ]
    },
    {
      "page": "GMS_Virtual-class",
      "title": "Class GMS_Virtual",
      "topics": [
        "GMS_Virtual-class"
      ]
    },
    {
      "page": "GMS-class",
      "title": "Class GMS",
      "topics": [
        "GMS",
        "GMS-class"
      ]
    },
    {
      "page": "HCC1395_Germline",
      "title": "Germline Calls",
      "topics": [
        "HCC1395_Germline"
      ]
    },
    {
      "page": "HCC1395_N",
      "title": "Normal BAM",
      "topics": [
        "HCC1395_N"
      ]
    },
    {
      "page": "HCC1395_T",
      "title": "Tumor BAM",
      "topics": [
        "HCC1395_T"
      ]
    },
    {
      "page": "hg19chr",
      "title": "hg19 chromosome boundaries",
      "topics": [
        "hg19chr"
      ]
    },
    {
      "page": "ideoView",
      "title": "Construct an ideogram",
      "topics": [
        "ideoView"
      ]
    },
    {
      "page": "lohSpec",
      "title": "Plot LOH data",
      "topics": [
        "lohSpec"
      ]
    },
    {
      "page": "lohView",
      "title": "Construct LOH chromosome plot",
      "topics": [
        "lohView"
      ]
    },
    {
      "page": "lolliplot",
      "title": "Construct a lolliplot",
      "topics": [
        "lolliplot"
      ]
    },
    {
      "page": "Lolliplot-class",
      "title": "Class Lolliplot",
      "topics": [
        "Lolliplot",
        "Lolliplot-class"
      ]
    },
    {
      "page": "LucCNseg",
      "title": "Truncated CN segments",
      "topics": [
        "LucCNseg"
      ]
    },
    {
      "page": "MutationAnnotationFormat_v1.0-class",
      "title": "Class MutationAnnotationFormat_v1.0",
      "topics": [
        "MutationAnnotationFormat_v1.0",
        "MutationAnnotationFormat_v1.0-class"
      ]
    },
    {
      "page": "MutationAnnotationFormat_v2.0-class",
      "title": "Class MutationAnnotationFormat_v2.0",
      "topics": [
        "MutationAnnotationFormat_v2.0",
        "MutationAnnotationFormat_v2.0-class"
      ]
    },
    {
      "page": "MutationAnnotationFormat_v2.1-class",
      "title": "Class MutationAnnotationFormat_v2.1",
      "topics": [
        "MutationAnnotationFormat_v2.1",
        "MutationAnnotationFormat_v2.1-class"
      ]
    },
    {
      "page": "MutationAnnotationFormat_v2.2-class",
      "title": "Class MutationAnnotationFormat_v2.2",
      "topics": [
        "MutationAnnotationFormat_v2.2",
        "MutationAnnotationFormat_v2.2-class"
      ]
    },
    {
      "page": "MutationAnnotationFormat_v2.3-class",
      "title": "Class MutationAnnotationFormat_v2.3",
      "topics": [
        "MutationAnnotationFormat_v2.3",
        "MutationAnnotationFormat_v2.3-class"
      ]
    },
    {
      "page": "MutationAnnotationFormat_v2.4-class",
      "title": "Class MutationAnnotationFormat_v2.4",
      "topics": [
        "MutationAnnotationFormat_v2.4",
        "MutationAnnotationFormat_v2.4-class"
      ]
    },
    {
      "page": "MutationAnnotationFormat_Virtual-class",
      "title": "Class MutationAnnotationFormat_Virtual",
      "topics": [
        "MutationAnnotationFormat_Virtual-class"
      ]
    },
    {
      "page": "MutationAnnotationFormat-class",
      "title": "Class MutationAnnotationFormat",
      "topics": [
        "MutationAnnotationFormat",
        "MutationAnnotationFormat-class"
      ]
    },
    {
      "page": "MutSpectra-class",
      "title": "Class MutSpectra",
      "topics": [
        "MutSpectra",
        "MutSpectra-class"
      ]
    },
    {
      "page": "PIK3CA",
      "title": "Subset MAF file for PIK3CA gene",
      "topics": [
        "PIK3CA"
      ]
    },
    {
      "page": "Rainfall-class",
      "title": "Class Rainfall",
      "topics": [
        "Rainfall",
        "Rainfall-class"
      ]
    },
    {
      "page": "SNPloci",
      "title": "Identity snps",
      "topics": [
        "SNPloci"
      ]
    },
    {
      "page": "TvTi",
      "title": "Construct transition-transversion plot",
      "topics": [
        "TvTi"
      ]
    },
    {
      "page": "VEP_v88-class",
      "title": "Class VEP_v88",
      "topics": [
        "VEP_v88",
        "VEP_v88-class"
      ]
    },
    {
      "page": "VEP_Virtual-class",
      "title": "Class VEP_Virtual",
      "topics": [
        "VEP_Virtual-class"
      ]
    },
    {
      "page": "VEP-class",
      "title": "Class VEP",
      "topics": [
        "VEP",
        "VEP-class"
      ]
    },
    {
      "page": "waterfall",
      "title": "Construct a oncoprint",
      "topics": [
        "waterfall"
      ]
    },
    {
      "page": "Waterfall-class",
      "title": "Class Waterfall",
      "topics": [
        "Waterfall",
        "Waterfall-class"
      ]
    },
    {
      "page": "writeData-methods",
      "title": "Method writeData",
      "topics": [
        "writeData",
        "writeData,GMS-method",
        "writeData,GMS_Virtual",
        "writeData,GMS_Virtual-method",
        "writeData,MutationAnnotationFormat-method",
        "writeData,MutationAnnotationFormat_Virtual",
        "writeData,MutationAnnotationFormat_Virtual-method",
        "writeData,VEP-method",
        "writeData,VEP_Virtual",
        "writeData,VEP_Virtual-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/GenVisR/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "farver",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "gtools",
    "hms",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "Intro.Rmd",
      "filename": "Intro.html",
      "title": "GenVisR: An introduction",
      "author": "Zachary Skidmore",
      "engine": "knitr::rmarkdown",
      "headings": [
        "GenVisR",
        "Install from Bioconductor",
        "Development",
        "Functions",
        "waterfall (mutation overview graphic)",
        "genCov (sequence coverage graphic)",
        "TvTi (transition/transversion graphic)",
        "cnSpec (copy altered cohort graphic)",
        "cnView (copy altered single sample graphic)",
        "covBars (sequencing coverage cohort)",
        "cnFreq (proportional copy number alterations)",
        "ideoView (ideogram graphic)",
        "lohSpec (Loss of Heterozygosity Spectrum)",
        "lohView (Loss of Heterozygosity View)",
        "compIdent (snp identity graphic)",
        "geneViz (Transcript Represenation)",
        "Hints",
        "Session Info"
      ],
      "created": "2018-04-27 16:22:51",
      "modified": "2022-09-04 21:52:56",
      "commits": 2
    },
    {
      "source": "waterfall_introduction.Rmd",
      "filename": "waterfall_introduction.html",
      "title": "waterfall: function introduction",
      "author": "Zachary Skidmore",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Functionality",
        "Loading primary input",
        "Filtering options",
        "The Mutation Burden",
        "Adding Clinical Data",
        "Adding Proportion sub-plots",
        "Adding cell labels",
        "Altering Plot Aesthetics",
        "Rearranging cells",
        "Tips and hints",
        "Types of output",
        "Saving plots",
        "Grob collisions"
      ],
      "created": "2016-03-11 23:22:35",
      "modified": "2018-04-27 16:22:51",
      "commits": 8
    }
  ],
  "_score": 10.164828534344482,
  "_indexed": true,
  "_nocasepkg": "genvisr",
  "_universes": [
    "bioc",
    "zlskidmore",
    "griffithlab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.45.0",
      "date": "2026-05-30T08:37:14.000Z",
      "distro": "noble",
      "commit": "eb94b6e2107602b25479bb9f1ff22107915dd2e6",
      "fileid": "ac1fd90bd746860f108860fd903fde98a18dabdf67f3cba4a3cee2ceb99c3fb5",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679065816"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.45.0",
      "date": "2026-05-30T08:36:33.000Z",
      "distro": "noble",
      "commit": "eb94b6e2107602b25479bb9f1ff22107915dd2e6",
      "fileid": "61dc3ea9e258c0c7b06847bfc7c1dc9853f5cc4603c4494dd58841bfa695ea45",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679065816"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.45.0",
      "date": "2026-05-30T12:03:23.000Z",
      "commit": "eb94b6e2107602b25479bb9f1ff22107915dd2e6",
      "fileid": "0c2a54939a6bbe788f5c84b1c9fe17869d7efb186b974bec9b8a9d066d0c0035",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679065816"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.45.0",
      "date": "2026-05-30T12:03:20.000Z",
      "commit": "eb94b6e2107602b25479bb9f1ff22107915dd2e6",
      "fileid": "df8ae172e79e84801aee68e3ec8470eb84682f984f21752d5e4462578e272b8f",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679065816"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.45.0",
      "date": "2026-05-30T08:37:08.000Z",
      "commit": "eb94b6e2107602b25479bb9f1ff22107915dd2e6",
      "fileid": "e3219bb373b40a2f5e46a90e02975d7c3dde1e66204f7a9249a4d094d443fffc",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679065816"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-05-30T08:35:38.000Z",
      "commit": "eb94b6e2107602b25479bb9f1ff22107915dd2e6",
      "fileid": "5eccd5848b8d785416bc0a05200dd1defb03382d653f44bf8e1750df52a39cbb",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679065816"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-05-30T08:35:48.000Z",
      "commit": "eb94b6e2107602b25479bb9f1ff22107915dd2e6",
      "fileid": "1ff4a9700f3a31d150cd2b73b05e6612adee1a3da23e5c9753a982e69d37b003",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679065816"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.45.0",
      "date": "2026-05-30T08:35:07.000Z",
      "commit": "eb94b6e2107602b25479bb9f1ff22107915dd2e6",
      "fileid": "07b7aedd157fbaa56f118d78b794315886eb61895032ff09009b53985f9b15a9",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679065816"
    }
  ]
}