{
  "_id": "6ac85b06de46216d5edd4657",
  "Package": "CNVRanger",
  "Version": "1.29.5",
  "Title": "Summarization and expression/phenotype association of CNV ranges",
  "Authors@R": "c(\nperson(\"Ludwig\", \"Geistlinger\", email = \"ludwig.geistlinger@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-2495-5464\")),\nperson(\"Vinicius Henrique\", \"da Silva\", role = \"aut\"),\nperson(\"Marcel\", \"Ramos\",\nrole = \"ctb\", comment = c(ORCID = \"0000-0002-3242-0582\")),\nperson(\"Levi\", \"Waldron\",\nrole = \"ctb\", comment = c(ORCID = \"0000-0003-2725-0694\"))\n)",
  "Description": "The CNVRanger package implements a comprehensive tool\nsuite for CNV analysis. This includes functionality for\nsummarizing individual CNV calls across a population, assessing\noverlap with functional genomic regions, and association\nanalysis with gene expression and quantitative phenotypes.",
  "License": "Artistic-2.0",
  "BugReports": "https://github.com/waldronlab/CNVRanger/issues",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "CopyNumberVariation, DifferentialExpression, GeneExpression,\nGenomeWideAssociation, GenomicVariation, Microarray, RNASeq,\nSNP",
  "Date": "2025-05-08",
  "Config/roxygen2/version": "8.1.0",
  "Config/pak/sysreqs": "libicu-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-08 20:53:34 UTC",
  "RemoteUrl": "https://github.com/bioc/CNVRanger",
  "RemoteRef": "HEAD",
  "RemoteSha": "2eec083295b3a79c29fe87cc365cf092c0175c9a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-09 02:31:30 UTC",
    "User": "root"
  },
  "Author": "Ludwig Geistlinger [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-2495-5464>),\nVinicius Henrique da Silva [aut],\nMarcel Ramos [ctb] (ORCID: <https://orcid.org/0000-0002-3242-0582>),\nLevi Waldron [ctb] (ORCID: <https://orcid.org/0000-0003-2725-0694>)",
  "Maintainer": "Ludwig Geistlinger <ludwig.geistlinger@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "CNVRanger_1.29.5.tar.gz",
  "_fileid": "https://r2.ropensci.org/60538468b2ffa2801a3aaa05824ff6b35039af916023ec83e0ca5120460a3a3e",
  "_filesize": 1964154,
  "_sha256": "60538468b2ffa2801a3aaa05824ff6b35039af916023ec83e0ca5120460a3a3e",
  "_expires": "2027-01-17T03:09:51.000Z",
  "_created": "2026-10-09T02:31:30.000Z",
  "_published": "2026-10-09T03:09:58.278Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37874364957",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 14
  },
  "_upstream": "https://github.com/bioc/CNVRanger",
  "_commit": {
    "id": "2eec083295b3a79c29fe87cc365cf092c0175c9a",
    "author": "lgeistlinger <ludwig.geistlinger@gmail.com>",
    "committer": "lgeistlinger <ludwig.geistlinger@gmail.com>",
    "message": "cnvOncoPrint: several improvements\n",
    "time": 1791492814
  },
  "_maintainer": {
    "name": "Ludwig Geistlinger",
    "email": "ludwig.geistlinger@gmail.com",
    "login": "lgeistlinger",
    "description": "",
    "uuid": 11871050,
    "orcid": "0000-0002-2495-5464"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 113641568528,
      "time": 231,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11592470030"
    },
    {
      "job": 113641568602,
      "time": 535,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11591638556"
    },
    {
      "job": 113641568662,
      "time": 537,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11592420970"
    },
    {
      "job": 113641568681,
      "time": 250,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": ""
    },
    {
      "job": 113641568557,
      "time": 321,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11592570706"
    },
    {
      "job": 113639483907,
      "time": 493,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11591868435"
    },
    {
      "job": 113641568630,
      "time": 280,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11591128762"
    },
    {
      "job": 113641568685,
      "time": 2200,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11593350611"
    },
    {
      "job": 113641568622,
      "time": 2230,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11593440225"
    },
    {
      "job": 113641568814,
      "time": 2178,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11592328763"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "RaggedExperiment",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "GDSArray",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SNPRelate",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "gdsfmt",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "lattice",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "qqman",
      "role": "Imports"
    },
    {
      "package": "rappdirs",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "AnnotationHub",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Btaurus.UCSC.bosTau6.masked",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Suggests"
    },
    {
      "package": "Gviz",
      "role": "Suggests"
    },
    {
      "package": "MultiAssayExperiment",
      "role": "Suggests"
    },
    {
      "package": "TCGAutils",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
      "role": "Suggests"
    },
    {
      "package": "curatedTCGAData",
      "role": "Suggests"
    },
    {
      "package": "ensembldb",
      "role": "Suggests"
    },
    {
      "package": "grid",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "regioneR",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "statmod",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 4
    },
    {
      "week": "2026-20",
      "n": 1
    },
    {
      "week": "2026-36",
      "n": 1
    },
    {
      "week": "2026-37",
      "n": 1
    },
    {
      "week": "2026-38",
      "n": 1
    },
    {
      "week": "2026-41",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.29.4",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.28.1",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "copynumbervariation",
    "differentialexpression",
    "geneexpression",
    "genomewideassociation",
    "genomicvariation",
    "microarray",
    "rnaseq",
    "snp",
    "bioconductor-package",
    "u24ca289073"
  ],
  "_stars": 8,
  "_contributors": [
    {
      "user": "viniciushdasilva",
      "count": 71,
      "uuid": 31412322
    },
    {
      "user": "lgeistlinger",
      "count": 20,
      "uuid": 11871050
    },
    {
      "user": "link-ny",
      "count": 20,
      "uuid": 4392950
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "lwaldron",
      "count": 1,
      "uuid": 639942
    },
    {
      "user": "viniciushsilva",
      "count": 1,
      "uuid": 162492488
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 474,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 548,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CNVRanger"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/waldronlab/cnvranger",
  "_searchresults": 18,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/CNVRanger.html",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/waldronlab/cnvranger",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "cnvEQTL",
    "cnvGWAS",
    "cnvOncoPrint",
    "generateGDS",
    "importLrrBaf",
    "plotEQTL",
    "plotManhattan",
    "plotRecurrentRegions",
    "populationRanges",
    "setupCnvGWAS"
  ],
  "_help": [
    {
      "page": "cnvEQTL",
      "title": "CNV-expression association analysis",
      "topics": [
        "cnvEQTL"
      ]
    },
    {
      "page": "cnvGWAS",
      "title": "Run the CNV-GWAS",
      "topics": [
        "cnvGWAS"
      ]
    },
    {
      "page": "cnvOncoPrint",
      "title": "OncoPrint plot for CNV regions",
      "topics": [
        "cnvOncoPrint"
      ]
    },
    {
      "page": "generateGDS",
      "title": "Produce CNV-GDS for the phenotyped samples",
      "topics": [
        "generateGDS"
      ]
    },
    {
      "page": "importLrrBaf",
      "title": "Import LRR and BAF from text files used in the CNV analysis",
      "topics": [
        "importLrrBaf"
      ]
    },
    {
      "page": "plotEQTL",
      "title": "Plot EQTL region",
      "topics": [
        "plotEQTL"
      ]
    },
    {
      "page": "plotManhattan",
      "title": "Manhattan Plot",
      "topics": [
        "plotManhattan"
      ]
    },
    {
      "page": "plotRecurrentRegions",
      "title": "Plot recurrent CNV regions",
      "topics": [
        "plotRecurrentRegions"
      ]
    },
    {
      "page": "populationRanges",
      "title": "Summarizing CNV ranges across a population",
      "topics": [
        "populationRanges"
      ]
    },
    {
      "page": "setupCnvGWAS",
      "title": "Setup the folders and files to run CNV-GWAS analysis",
      "topics": [
        "setupCnvGWAS"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CNVRanger/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "calibrate",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DelayedArray",
    "digest",
    "edgeR",
    "formatR",
    "futile.logger",
    "futile.options",
    "GDSArray",
    "gdsfmt",
    "generics",
    "GenomeInfoDb",
    "GenomicRanges",
    "glue",
    "httr",
    "IRanges",
    "jsonlite",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mime",
    "openssl",
    "plyr",
    "qqman",
    "R6",
    "RaggedExperiment",
    "rappdirs",
    "Rcpp",
    "reshape2",
    "RhpcBLASctl",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "SeqArray",
    "Seqinfo",
    "snow",
    "SNPRelate",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "UCSC.utils",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "CNVRanger.Rmd",
      "filename": "CNVRanger.html",
      "title": "Summarization and quantitative trait analysis of CNV ranges",
      "author": "Vinicius Henrique da Silva, Ludwig Geistlinger",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Applicability and Scope",
        "Key functions",
        "Reading and accessing CNV data",
        "Input data format",
        "Representation as a GRangesList",
        "Representation as a RaggedExperiment",
        "Summarizing individual CNV calls across a population",
        "Trimming low-density areas",
        "Reciprocal overlap",
        "Identifying recurrent regions",
        "Overlap analysis of CNVs with functional genomic regions",
        "Finding and illustrating overlaps",
        "Overlap permutation test",
        "CNV-expression association analysis",
        "Application to individual CNV and RNA-seq assays",
        "Application to TCGA data stored in a MultiAssayExperiment",
        "CNV-phenotype association analysis",
        "Setting up a CNV-GWAS",
        "Running a CNV-GWAS",
        "Producing a GDS file in advance",
        "Using relative signal intensities",
        "Session info",
        "References"
      ],
      "created": "2018-10-17 23:32:16",
      "modified": "2026-09-15 23:59:13",
      "commits": 53
    }
  ],
  "_score": 6.547528576459782,
  "_indexed": true,
  "_nocasepkg": "cnvranger",
  "_universes": [
    "bioc",
    "lgeistlinger",
    "waldronlab"
  ],
  "_previous": "1.29.4",
  "_binaries": [
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.4",
      "date": "2026-09-16T06:28:04.000Z",
      "commit": "e550d9a9d4db27ac0caeaeab2793c9e72c74e0ac",
      "fileid": "https://r2.ropensci.org/4b35d15f356212bf1ea4c3ddae31e6b4e63a1b0820fa980975e4b9afc98dcb88",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35062668494"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.29.5",
      "date": "2026-10-09T02:38:18.000Z",
      "distro": "resolute",
      "commit": "2eec083295b3a79c29fe87cc365cf092c0175c9a",
      "fileid": "https://r2.ropensci.org/23a69177e39bd9857bc8982b28a23c5dd97471544b1bdf424a88656bfc2aea3c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37874364957"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.29.5",
      "date": "2026-10-09T02:38:15.000Z",
      "distro": "resolute",
      "commit": "2eec083295b3a79c29fe87cc365cf092c0175c9a",
      "fileid": "https://r2.ropensci.org/af543c107a0c4ebad75a780dc90cc5df2ee457b9a346971b6c72d15c01d7d71e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37874364957"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.29.5",
      "date": "2026-10-09T02:39:34.000Z",
      "commit": "2eec083295b3a79c29fe87cc365cf092c0175c9a",
      "fileid": "https://r2.ropensci.org/36245fadbb13efb7e5963ce3aa5384c4d08b3aa3106d808f3636eac3bd644a2b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37874364957"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.29.5",
      "date": "2026-10-09T02:36:47.000Z",
      "commit": "2eec083295b3a79c29fe87cc365cf092c0175c9a",
      "fileid": "https://r2.ropensci.org/0d02eb152cf3c9fcac38e075fda0764b3a518b1a4300958e32d2148820a05993",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37874364957"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.29.5",
      "date": "2026-10-09T03:05:54.000Z",
      "commit": "2eec083295b3a79c29fe87cc365cf092c0175c9a",
      "fileid": "https://r2.ropensci.org/8fcba88bbb4230d9c855d97dd02a3325b5078819f9bd9d67018ba8ba5fd1f098",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37874364957"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.29.5",
      "date": "2026-10-09T03:06:37.000Z",
      "commit": "2eec083295b3a79c29fe87cc365cf092c0175c9a",
      "fileid": "https://r2.ropensci.org/7b2ea4001f488b162271fb775eb93225a5004c3d66f119f6fcff9a02675e8652",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37874364957"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.29.5",
      "date": "2026-10-09T03:05:47.000Z",
      "commit": "2eec083295b3a79c29fe87cc365cf092c0175c9a",
      "fileid": "https://r2.ropensci.org/c83eedea0dcc124fa5756b77f6f675a3f1e3758f9378b2d510c7a6ef5ba87669",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37874364957"
    }
  ]
}