{ "_id": "6a218ef5cd65a98ecbd388d4", "Package": "rCNV", "Type": "Package", "Title": "Detect Copy Number Variants from SNPs Data", "Version": "1.5.900", "Date": "2026-06-03", "Language": "en-US", "Authors@R": "c(person(given=\"Piyal\",family=\"Karunarathne\", email=\"piyalkarumail@yahoo.com\", role = c(\"aut\", \"cre\"),comment = c(ORCID = \"0000-0002-1934-145X\")),person(given=\"Qiujie\",family=\"Zhou\", email=\"qiujie.zhou@ebc.uu.se\", role = c(\"aut\"),comment = c(ORCID = \"0000-0001-7351-2371\")),person(\"Klaus\", \"Schliep\", email=\"klaus.schliep@gmail.com\", role = c(\"aut\"), comment = c(ORCID = \"0000-0003-2941-0161\")),person(given=\"Pascal\", family=\"Milesi\", role = \"aut\",comment = c(ORCID = \"0000-0001-8580-4291\")))", "Maintainer": "Piyal Karunarathne ", "Description": "Functions in this package will import filtered variant\ncall format (VCF) files of SNPs data and generate data sets to\ndetect copy number variants, visualize them and do downstream\nanalyses with copy number variants(e.g. Environmental\nassociation analyses).", "License": "AGPL (>= 3)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "biocViews": "GenomicVariation, Sequencing, CopyNumberVariation", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "URL": "https://piyalkarum.github.io/rCNV/,\nhttps://cran.r-project.org/package=rCNV", "Additional_repositories": "https://bioconductor.org/packages/release/bioc", "BugReports": "https://github.com/piyalkarum/rCNV/issues", "Packaged": { "Date": "2026-06-04 14:34:53 UTC", "User": "root" }, "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://piyalkarum.r-universe.dev", "Date/Publication": "2026-06-04 13:18:28 UTC", "RemoteUrl": "https://github.com/piyalkarum/rcnv", "RemoteRef": "HEAD", "RemoteSha": "81c225fc0f58fad2b370eba8cf464c1eacb92ccc", "NeedsCompilation": "no", "Author": "Piyal Karunarathne [aut, cre] (ORCID:\n),\nQiujie Zhou [aut] (ORCID: ),\nKlaus Schliep [aut] (ORCID: ),\nPascal Milesi [aut] (ORCID: )", "MD5sum": "d33fdafcf367feabd1477b10bdd96c8d", "_user": "piyalkarum", "_type": "src", "_file": "rCNV_1.5.900.tar.gz", "_fileid": "ea19bfec8f4a0241d8f5e529903648c35cc4c23c3dee39dcdeb31620c5aa840a", "_filesize": 3714733, "_sha256": "ea19bfec8f4a0241d8f5e529903648c35cc4c23c3dee39dcdeb31620c5aa840a", "_created": "2026-06-04T14:34:53.000Z", "_published": "2026-06-04T14:43:01.049Z", "_distro": "noble", "_jobs": [ { "job": 79542615850, "time": 366, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7414475070" }, { "job": 79542615929, "time": 346, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7414466903" }, { "job": 79542615936, "time": 355, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7414452695" }, { "job": 79542616210, "time": 316, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7414435924" }, { "job": 79541375864, "time": 358, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7414316307" }, { "job": 79542616011, "time": 172, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7414392809" }, { "job": 79542615884, "time": 308, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7414451038" }, { "job": 79542616070, "time": 284, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7414440119" }, { "job": 79542615803, "time": 266, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7414432996" } ], "_buildurl": "https://github.com/r-universe/piyalkarum/actions/runs/26958268796", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/piyalkarum/rcnv", "_commit": { "id": "81c225fc0f58fad2b370eba8cf464c1eacb92ccc", "author": "piyalkarum ", "committer": "piyalkarum ", "message": "wgs+page updated\n", "time": 1780579108 }, "_maintainer": { "name": "Piyal Karunarathne", "email": "piyalkarumail@yahoo.com", "login": "piyalkarum", "orcid": "0000-0002-1934-145X", "twitter": "@kaint_w8_karu", "description": "I am an evolutionary ecologist/geneticist. I develop statistical models and bioinformatics tools for biodiversity and evolutionary studies.", "uuid": 48254643 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "colorspace", "role": "Imports" }, { "package": "R.utils", "role": "Imports" }, { "package": "qgraph", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "extraDistr", "role": "Imports" }, { "package": "fitdistrplus", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "piyalkarum", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-15", "n": 2 }, { "week": "2026-23", "n": 3 } ], "_tags": [], "_topics": [ "genomicvariation", "sequencing", "copynumbervariation", "cnv-analysis", "copy-number-variation", "gene-duplication", "genetics", "genomics", "landscape-genetics", "snps" ], "_stars": 6, "_contributors": [ { "user": "piyalkarum", "count": 205, "uuid": 48254643 }, { "user": "klausvigo", "count": 6, "uuid": 3372431 } ], "_userbio": { "uuid": 48254643, "type": "user", "name": "Piyal Karunarathne", "description": "I am an evolutionary ecologist/geneticist. I develop statistical models and bioinformatics tools for biodiversity and evolutionary studies." }, "_downloads": { "count": 166, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rCNV" }, "_devurl": "https://github.com/piyalkarum/rcnv", "_pkgdown": "https://piyalkarum.github.io/rCNV/", "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/rCNV.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/piyalkarum/rcnv", "_realowner": "piyalkarum", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2022-04-06" }, { "version": "1.1.0", "date": "2022-10-26" }, { "version": "1.2.0", "date": "2023-08-08" }, { "version": "1.3.0", "date": "2024-09-20" } ], "_exports": [ "ad.correct", "allele.freq", "allele.info", "allele.info.WGS", "allele.info.WGS.GCcor", "allele.info.WGS3", "cnv", "cpm.normal", "depthVsSample", "dup.plot", "dup.validate", "dupGet", "exportVCF", "get.miss", "gt.format", "h.zygosity", "hetTgen", "maf", "norm.fact", "power.bias", "readVCF", "relatedness", "sig.hets", "sim.als", "vcf.stat", "vst", "vstPermutation" ], "_datasets": [ { "name": "ADnorm", "title": "Normalized allele depth example data", "object": "ADnorm", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ADtable", "title": "Allele Depth (AD) example data", "object": "ADtable", "class": [ "data.frame" ], "fields": [ "CHROM", "POS", "ID", "ALT", "KKOGR07_0005_combo", "KKOGR07_0006", "KKOGR07_0007", "KKOGR07_0008", "KKOGR07_0009", "KKOGR07_0011_combo", "KKOGR07_0013", "KKOGR07_0014", "KKOGR07_0015_combo", "KKOGR07_0016", "KKOGR07_0018", "KKOGR07_0019", "KKOGR07_0021", "KKOGR07_0022", "KKOGR07_0023", "KKOGR07_0024", "KKOGR07_0025_combo", "KKOGR07_0027", "KKOGR07_0028", "KKOGR07_0029", "KKOGR07_0030", "KKOGR07_0031", "KKOGR07_0032", "KKOGR07_0033", "KKOGR07_0034", "KKOGR07_0035", "KKOGR07_0036", "KKOGR07_0037", "KKOGR07_0038", "KKOGR07_0039", "KKOGR07_0040", "KKOGR07_0041", "KKOGR07_0042", "KKOGR07_0043_combo", "KKOGR07_0044", "KKOGR07_0045", "KKOGR07_0046", "KKOGR07_0047", "KKOGR07_0048", "KKOGR07_0049", "KKOGR07_0050", "KKOGR07_0051", "KKOGR07_0052", "KKOGR07_0053", "KKOGR07_0054", "KKOGR07_0055", "KKOGR07_0056", "KKOGR07_0057", "KKOGR07_0058", "KKOGR07_0059", "KKOGR07_0060", "KKOGR07_0061", "KKOGR07_0062", "KKOGR07_0063", "KKOGR07_0064", "KKOKT10_0002", "KKOKT10_0003", "KKOKT10_0004", "KKOKT10_0005", "KKOKT10_0006", "KKOKT10_0008", "KKOKT10_0009", "KKOKT10_0010", "KKOKT10_0011", "KKOKT10_0012", "KKOKT10_0014_combo", "KKOKT10_0015_combo", "KKOKT10_0017", "KKOKT10_0019", "KKOKT10_0020", "KKOKT10_0021", "KKOKT10_0023_combo", "KKOKT10_0024", "KKOKT10_0025", "KKOKT10_0026_combo", "KKOKT10_0027", "KKOKT10_0028", "KKOKT10_0029", "KKOKT10_0031", "KKOKT10_0032", "KKOKT10_0033", "KKOKT10_0034", "KKOKT10_0036", "KKOKT10_0037", "KKOKT10_0040", "KKOKT10_0042", "KKOKT10_0044", "KKOKT10_0045", "KKOKT10_0046", "KKOKT10_0048", "KKOKT10_0049", "KKOKT10_0053", "KKOKT10_0057", "KKOKT10_0059", "KKOKT10_0062", "KKOKT10_0063", "KKOKT10_0064", "KKOKT10_0065", "KKOKT10_0066", "KKOKT10_0067", "KKOKT10_0069", "KKOKT10_0070", "KKOKT10_0071", "KKOKT10_0075", "KKOKT10_0077" ], "rows": 3000, "table": true, "tojson": true }, { "name": "alleleINF", "title": "Allele info example data", "object": "alleleINF", "class": [ "data.frame" ], "fields": [ "CHROM", "POS", "ID", "NHet", "propHet", "medRatio", "NHomRef", "NHomAlt", "propHomAlt", "Nsamp", "pAll", "pHet", "fis", "z.het", "z.05", "z.all", "chi.het", "chi.05", "chi.all", "z.het.sum", "z.05.sum", "z.all.sum", "chi.het.sum", "chi.05.sum", "chi.all.sum", "eH.pval", "eH.delta", "cv" ], "rows": 2857, "table": true, "tojson": true } ], "_help": [ { "page": "rCNV-package", "title": "rCNV: Detect Copy Number Variants from SNP Data", "topics": [ "rCNV-package", "rCNV" ] }, { "page": "ad.correct", "title": "Correct allele depth values", "topics": [ "ad.correct" ] }, { "page": "ADnorm", "title": "Normalized allele depth example data", "topics": [ "ADnorm" ] }, { "page": "ADtable", "title": "Allele Depth (AD) example data", "topics": [ "ADtable" ] }, { "page": "allele.freq", "title": "Generate allele frequency table for individuals or populations", "topics": [ "allele.freq" ] }, { "page": "allele.info", "title": "Get allele information for duplicate detection", "topics": [ "allele.info" ] }, { "page": "allele.info.WGS", "title": "ClrCNV: multicopy detection for WGS", "topics": [ "allele.info.WGS" ] }, { "page": "allele.info.WGS.GCcor", "title": "Allele Information with GC-Bias Correction for WGS Data", "topics": [ "allele.info.WGS.GCcor" ] }, { "page": "allele.info.WGS3", "title": "Allele Information for WGS Data (No GC Correction)", "topics": [ "allele.info.WGS3" ] }, { "page": "alleleINF", "title": "Allele info example data", "topics": [ "alleleINF" ] }, { "page": "cnv", "title": "Find CNVs from deviants", "topics": [ "cnv" ] }, { "page": "cpm.normal", "title": "Calculate normalized depth for alleles", "topics": [ "cpm.normal" ] }, { "page": "depthVsSample", "title": "Simulate median allele ratios for varying number of samples and depth values", "topics": [ "depthVsSample" ] }, { "page": "dup.plot", "title": "Plot classified SNPs into deviants/CNVs and non-deviants/non-CNVs", "topics": [ "dup.plot" ] }, { "page": "dup.validate", "title": "Validate detected deviants/cnvs", "topics": [ "dup.validate" ] }, { "page": "dupGet", "title": "Detect deviants from SNPs; classify SNPs", "topics": [ "dupGet" ] }, { "page": "exportVCF", "title": "Export VCF files", "topics": [ "exportVCF" ] }, { "page": "get.miss", "title": "Get missingness of individuals in raw vcf", "topics": [ "get.miss" ] }, { "page": "gt.format", "title": "Format genotype for BayEnv and BayPass", "topics": [ "gt.format" ] }, { "page": "h.zygosity", "title": "Determine per sample heterozygosity and inbreeding coefficient", "topics": [ "h.zygosity" ] }, { "page": "hetTgen", "title": "Generate allele depth or genotype table", "topics": [ "hetTgen" ] }, { "page": "maf", "title": "Remove MAF allele", "topics": [ "maf" ] }, { "page": "norm.fact", "title": "Calculate normalization factor for each sample", "topics": [ "norm.fact" ] }, { "page": "power.bias", "title": "Simulate and plot detection power of bias in allele ratios", "topics": [ "power.bias" ] }, { "page": "readVCF", "title": "Import VCF file", "topics": [ "readVCF" ] }, { "page": "relatedness", "title": "Determine pairwise relatedness", "topics": [ "relatedness" ] }, { "page": "sig.hets", "title": "Identify significantly different heterozygotes from SNPs data", "topics": [ "sig.hets" ] }, { "page": "sim.als", "title": "Simulate Allele Frequencies", "topics": [ "sim.als" ] }, { "page": "vcf.stat", "title": "Get sequencing quality statistics of raw VCF files (with GatK generated vcf files only)", "topics": [ "vcf.stat" ] }, { "page": "vst", "title": "Calculate population-wise Vst", "topics": [ "vst" ] }, { "page": "vstPermutation", "title": "Run permutation on Vst", "topics": [ "vstPermutation" ] } ], "_pkglogo": "https://github.com/piyalkarum/rcnv/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/piyalkarum/rcnv/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "bslib", "cachem", "checkmate", "cigarillo", "cli", "cluster", "codetools", "colorspace", "corpcor", "cpp11", "crayon", "curl", "data.table", "DelayedArray", "digest", "evaluate", "extraDistr", "farver", "fastmap", "fdrtool", "fitdistrplus", "fontawesome", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "ggplot2", "glasso", "glue", "GPArotation", "gridExtra", "gtable", "gtools", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "httr", "igraph", "IRanges", "isoband", "jpeg", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "lattice", "lavaan", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "mnormt", "nlme", "nnet", "numDeriv", "openssl", "pbapply", "pbivnorm", "pkgconfig", "plyr", "png", "psych", "qgraph", "quadprog", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RCurl", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "rpart", "Rsamtools", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tinytex", "UCSC.utils", "vctrs", "viridisLite", "withr", "xfun", "XML", "XVector", "yaml" ], "_score": 3.7781512503836434, "_indexed": true, "_nocasepkg": "rcnv", "_universes": [ "piyalkarum" ], "_previous": "1.4.900", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.900", "date": "2026-06-04T14:38:27.000Z", "distro": "noble", "commit": "81c225fc0f58fad2b370eba8cf464c1eacb92ccc", "fileid": "944f52b5593913543f408c7cf8b460183640650ed0ae3d56dc5da89b5321a7c2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/piyalkarum/actions/runs/26958268796" }, { "r": "4.6.0", "os": "linux", "version": "1.5.900", "date": "2026-06-04T14:38:29.000Z", "distro": "noble", "commit": "81c225fc0f58fad2b370eba8cf464c1eacb92ccc", "fileid": "7e7dd026d32907d2beb33ec2aef39ad16d26ed3ada68d11db8a700edd40b45db", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/piyalkarum/actions/runs/26958268796" }, { "r": "4.5.3", "os": "mac", "version": "1.5.900", "date": "2026-06-04T14:38:13.000Z", "commit": "81c225fc0f58fad2b370eba8cf464c1eacb92ccc", "fileid": "63377bba86d4d4373c67b1a8f2a863dab81d85f1eb103321b8126cbb67a50091", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/piyalkarum/actions/runs/26958268796" }, { "r": "4.6.0", "os": "mac", "version": "1.5.900", "date": "2026-06-04T14:37:50.000Z", "commit": "81c225fc0f58fad2b370eba8cf464c1eacb92ccc", "fileid": "b82c6c02b1c53cbadf4a35753f9cb73afac7c1506928876c9ceaa926556a14f2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/piyalkarum/actions/runs/26958268796" }, { "r": "4.6.0", "os": "wasm", "version": "1.5.900", "date": "2026-06-04T14:38:30.000Z", "commit": "81c225fc0f58fad2b370eba8cf464c1eacb92ccc", "fileid": "590ea822a6f6efc43d753d66c52f764f8db6bfa5b7e0113d7e67e909df0f5846", "status": "success", "buildurl": "https://github.com/r-universe/piyalkarum/actions/runs/26958268796" }, { "r": "4.7.0", "os": "win", "version": "1.5.900", "date": "2026-06-04T14:37:17.000Z", "commit": "81c225fc0f58fad2b370eba8cf464c1eacb92ccc", "fileid": "7c9dbd8eb14cc9a9ef483dcf988b7a22a0aedf2f42656f7a6688cb3c29888d54", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/piyalkarum/actions/runs/26958268796" }, { "r": "4.5.3", "os": "win", "version": "1.5.900", "date": "2026-06-04T14:37:22.000Z", "commit": "81c225fc0f58fad2b370eba8cf464c1eacb92ccc", "fileid": "7ee35f0466f7efc9e4dd6340e939f65c29835fe16f2dac00708079f68e2c30a7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/piyalkarum/actions/runs/26958268796" }, { "r": "4.6.0", "os": "win", "version": "1.5.900", "date": "2026-06-04T14:36:59.000Z", "commit": "81c225fc0f58fad2b370eba8cf464c1eacb92ccc", "fileid": "befb99271339cd7ce2ec1c281c702ecee4f0a0005603ec1b04c325566a3d6415", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/piyalkarum/actions/runs/26958268796" } ] }