{ "_id": "6a1ad86b1d7bb097a09e6bea", "Package": "CNVRanger", "Version": "1.29.1", "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", "RoxygenNote": "7.2.3", "Date": "2025-05-08", "Config/pak/sysreqs": "libicu-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-29 21:08:50 UTC", "RemoteUrl": "https://github.com/bioc/CNVRanger", "RemoteRef": "HEAD", "RemoteSha": "53d628f90b7924c5d1de7e7139e30cee76cae782", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:53:05 UTC", "User": "root" }, "Author": "Ludwig Geistlinger [aut, cre] (ORCID:\n),\nVinicius Henrique da Silva [aut],\nMarcel Ramos [ctb] (ORCID: ),\nLevi Waldron [ctb] (ORCID: )", "Maintainer": "Ludwig Geistlinger ", "MD5sum": "0ae22ecf76ae26c43347b1f7ae3b120a", "_user": "bioc", "_type": "src", "_file": "CNVRanger_1.29.1.tar.gz", "_fileid": "10eff0c38d55fbeec67bf6e4188c4b43023589cfdcf3e2c9f4cbc4810bd02832", "_filesize": 1968709, "_sha256": "10eff0c38d55fbeec67bf6e4188c4b43023589cfdcf3e2c9f4cbc4810bd02832", "_created": "2026-05-30T08:53:05.000Z", "_published": "2026-05-30T12:30:35.714Z", "_jobs": [ { "job": 78637899863, "time": 346, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307011310" }, { "job": 78637899887, "time": 482, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307024961" }, { "job": 78637899885, "time": 560, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307032946" }, { "job": 78637899889, "time": 274, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308177309" }, { "job": 78637899891, "time": 223, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308172467" }, { "job": 78637357436, "time": 577, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306974456" }, { "job": 78637899847, "time": 322, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307008565" }, { "job": 78637899850, "time": 1102, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307085518" }, { "job": 78637899858, "time": 1197, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307094506" }, { "job": 78637899870, "time": 1084, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307083720" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679536364", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CNVRanger", "_commit": { "id": "53d628f90b7924c5d1de7e7139e30cee76cae782", "author": "LiNk-NY ", "committer": "LiNk-NY ", "message": "version bump 1.29.1\n", "time": 1777496930 }, "_maintainer": { "name": "Ludwig Geistlinger", "email": "ludwig.geistlinger@gmail.com", "login": "lgeistlinger", "description": "", "uuid": 11871050, "orcid": "0000-0002-2495-5464" }, "_distro": "noble", "_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 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.29.1", "bioc": "3.24" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23" } ], "_topics": [ "copynumbervariation", "differentialexpression", "geneexpression", "genomewideassociation", "genomicvariation", "microarray", "rnaseq", "snp", "bioconductor-package", "u24ca289073" ], "_stars": 8, "_contributors": [ { "user": "viniciushdasilva", "count": 71, "uuid": 31412322 }, { "user": "link-ny", "count": 20, "uuid": 4392950 }, { "user": "lgeistlinger", "count": 16, "uuid": 11871050 }, { "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", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 401, "source": "https://www.bioconductor.org/packages/stats/bioc/CNVRanger" }, "_mentions": 1, "_devurl": "https://github.com/waldronlab/cnvranger", "_searchresults": 13, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CNVRanger.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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": "2025-05-08 16:17:11", "commits": 52 } ], "_score": 5.862131379313037, "_indexed": true, "_nocasepkg": "cnvranger", "_universes": [ "bioc", "lgeistlinger", "waldronlab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.1", "date": "2026-05-30T08:59:13.000Z", "distro": "noble", "commit": "53d628f90b7924c5d1de7e7139e30cee76cae782", "fileid": "6a549852dbc89953ae160d0c5192a0cc11501c2ec6d94ff6e5a7836af3b0ec17", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679536364" }, { "r": "4.6.0", "os": "linux", "version": "1.29.1", "date": "2026-05-30T09:00:04.000Z", "distro": "noble", "commit": "53d628f90b7924c5d1de7e7139e30cee76cae782", "fileid": "d838d74282897d0cd7370c40edeeb08fc2b8551637669fd852315d3fd9b5cb51", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679536364" }, { "r": "4.5.3", "os": "mac", "version": "1.29.1", "date": "2026-05-30T12:28:32.000Z", "commit": "53d628f90b7924c5d1de7e7139e30cee76cae782", "fileid": "9f3aee7c92cddf21251c82926cd25e879c65684209dcceafeed700571c68ab38", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679536364" }, { "r": "4.6.0", "os": "mac", "version": "1.29.1", "date": "2026-05-30T12:27:55.000Z", "commit": "53d628f90b7924c5d1de7e7139e30cee76cae782", "fileid": "058d75e8d0d026a65280cc90b1885bc143def7955c0329af0054412029e15d43", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679536364" }, { "r": "4.6.0", "os": "wasm", "version": "1.29.1", "date": "2026-05-30T08:58:59.000Z", "commit": "53d628f90b7924c5d1de7e7139e30cee76cae782", "fileid": "2a472a66ba17d4125c5fb9cffbda66df9eb6b5e520c967d790a2718195b211ab", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679536364" }, { "r": "4.7.0", "os": "win", "version": "1.29.1", "date": "2026-05-30T09:09:02.000Z", "commit": "53d628f90b7924c5d1de7e7139e30cee76cae782", "fileid": "46f3c93662bc1743b322716eab843ce986aff7a0090d613cb8c501360b26ece7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679536364" }, { "r": "4.5.3", "os": "win", "version": "1.29.1", "date": "2026-05-30T09:10:44.000Z", "commit": "53d628f90b7924c5d1de7e7139e30cee76cae782", "fileid": "3e7c1ade4cabeefea11e7773bbdd8e152f574c51b36ca1f17d835a24d5fc5a5a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679536364" }, { "r": "4.6.0", "os": "win", "version": "1.29.1", "date": "2026-05-30T09:09:12.000Z", "commit": "53d628f90b7924c5d1de7e7139e30cee76cae782", "fileid": "8facef61175c936b7c64dab56f9a0cdb12af6d4cc3a4a4fb0dae5ab41fe1c761", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679536364" } ] }