{ "_id": "6a1aeb5c1d7bb097a09f3d0e", "Package": "CNVrd2", "Type": "Package", "Title": "CNVrd2: a read depth-based method to detect and genotype complex\ncommon copy number variants from next generation sequencing\ndata.", "Version": "1.51.0", "Date": "2014-10-04", "Author": "Hoang Tan Nguyen, Tony R Merriman and Mik Black", "VignetteBuilder": "knitr", "Maintainer": "Hoang Tan Nguyen ", "Description": "CNVrd2 uses next-generation sequencing data to measure\nhuman gene copy number for multiple samples, indentify SNPs\ntagging copy number variants and detect copy number polymorphic\ngenomic regions.", "License": "GPL-2", "biocViews": "CopyNumberVariation, SNP, Sequencing, Software, Coverage,\nLinkageDisequilibrium, Clustering.", "Collate": "AllClasses.R AllGenerics.R countReadInWindow.R\nsegmentSamples.R segmentSamplesUsingPopInformation.R\nidentifyPolymorphicRegion.R plotPolymorphicRegion.R\nemnormalCNV.R groupCNVs.R searchGroupCNVs.R groupBayesianCNVs.R\nplotCNVrd2.R calculateLDSNPandCNV.R", "URL": "https://github.com/hoangtn/CNVrd2", "Packaged": { "Date": "2026-05-30 09:39:50 UTC", "User": "root" }, "Config/pak/sysreqs": "make jags libbz2-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:38:25 UTC", "RemoteUrl": "https://github.com/bioc/CNVrd2", "RemoteRef": "HEAD", "RemoteSha": "1e605d700f5051cb9e650c2ac47f38f482c5e37d", "NeedsCompilation": "no", "MD5sum": "e30b6af8ee99f3911701018ee19afc5c", "_user": "bioc", "_type": "src", "_file": "CNVrd2_1.51.0.tar.gz", "_fileid": "0f2456db2db68dbc7807a61e1578723c2d45fe45a113e6f512f4c83126bf4919", "_filesize": 2467619, "_sha256": "0f2456db2db68dbc7807a61e1578723c2d45fe45a113e6f512f4c83126bf4919", "_created": "2026-05-30T09:39:50.000Z", "_published": "2026-05-30T13:51:24.932Z", "_jobs": [ { "job": 78640262189, "time": 200, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307371990" }, { "job": 78640262191, "time": 256, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307377088" }, { "job": 78640262187, "time": 338, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307384046" }, { "job": 78640262196, "time": 173, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308645134" }, { "job": 78640262198, "time": 209, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308648995" }, { "job": 78637528305, "time": 3202, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7307247428" }, { "job": 78640262199, "time": 154, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307367623" }, { "job": 78640262203, "time": 224, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307374976" }, { "job": 78640262222, "time": 231, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307376926" }, { "job": 78640262206, "time": 206, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307373279" } ], "_bioccheck": { "error": 3, "warning": 6, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679596720", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CNVrd2", "_commit": { "id": "1e605d700f5051cb9e650c2ac47f38f482c5e37d", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379905 }, "_maintainer": { "name": "Hoang Tan Nguyen", "email": "hoangtannguyenvn@gmail.com", "login": "hoangtn", "description": "", "uuid": 4650940 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "VariantAnnotation", "role": "Depends" }, { "package": "parallel", "role": "Depends" }, { "package": "rjags", "role": "Depends" }, { "package": "ggplot2", "role": "Depends" }, { "package": "gridExtra", "role": "Depends" }, { "package": "DNAcopy", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.51.0", "bioc": "3.24" }, { "branch": "release", "version": "1.50.0", "bioc": "3.23" } ], "_topics": [ "copynumbervariation", "snp", "sequencing", "software", "coverage", "linkagedisequilibrium", "clustering.", "jags", "cpp" ], "_stars": 3, "_contributors": [ { "user": "hoangtn", "count": 67, "uuid": 4650940 }, { "user": "vngs", "count": 7, "uuid": 2603197 }, { "user": "theboocock", "count": 5, "uuid": 605678 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 406, "source": "https://www.bioconductor.org/packages/stats/bioc/CNVrd2" }, "_mentions": 7, "_devurl": "https://github.com/hoangtn/cnvrd2", "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CNVrd2.html", "extra/contents.json", "manual.pdf" ], "_homeurl": "https://github.com/hoangtn/cnvrd2", "_realowner": "bioc", "_cranurl": false, "_exports": [ "calculateLDSNPandCNV", "countReadInWindow", "emnormalCNV", "groupBayesianCNVs", "groupCNVs", "identifyPolymorphicRegion", "plotCNVrd2", "plotPolymorphicRegion", "searchGroupCNVs", "segmentSamples", "segmentSamplesUsingPopInformation" ], "_datasets": [ { "name": "ccl3l1data", "title": "Data of CCL3L1 gene (The 1000 Genomes Project)", "object": "ccl3l1data", "file": "ccl3l1data.txt.gz", "class": [ "data.frame" ], "fields": [ "Name", "Pop", "SS", "CN" ], "rows": 1917, "table": true, "tojson": true }, { "name": "copynumberGroups", "title": "MXL population data (The 1000 Genomes Project)", "object": "fcgr3bMXL", "file": "fcgr3bMXL.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "objectCNVrd2", "title": "MXL population data (The 1000 Genomes Project)", "object": "fcgr3bMXL", "file": "fcgr3bMXL.RData", "class": [ "CNVrd2" ], "fields": [], "table": false, "tojson": false }, { "name": "resultSegment", "title": "MXL population data (The 1000 Genomes Project)", "object": "fcgr3bMXL", "file": "fcgr3bMXL.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "CNVrd2-package", "title": "CNVrd2", "topics": [ "CNVrd2-package" ] }, { "page": "calculateLDSNPandCNV", "title": "calculateLDSNPandCNV", "topics": [ "calculateLDSNPandCNV" ] }, { "page": "ccl3l1data", "title": "Data of CCL3L1 gene (The 1000 Genomes Project)", "topics": [ "ccl3l1data" ] }, { "page": "clusteringCNVs-class", "title": "Class '\"clusteringCNVs\"'", "topics": [ "clusteringCNVs-class", "emnormalCNV,clusteringCNVs-method", "groupCNVs,clusteringCNVs-method", "objectCluster", "searchGroupCNVs,clusteringCNVs-method" ] }, { "page": "CNVrd2-class", "title": "Class '\"CNVrd2\"'", "topics": [ "CNVrd2-class", "countReadInWindow,CNVrd2-method", "plotCNVrd2,CNVrd2-method" ] }, { "page": "countReadInWindow", "title": "Obtain read counts in constant windows.", "topics": [ "countReadInWindow" ] }, { "page": "countReadInWindow-methods", "title": "Method 'countReadInWindow'", "topics": [ "countReadInWindow-methods" ] }, { "page": "emnormalCNV", "title": "Implement the EM algorithm", "topics": [ "emnormalCNV" ] }, { "page": "emnormalCNV-methods", "title": "Method 'emnormalCNV'", "topics": [ "emnormalCNV-methods" ] }, { "page": "fcgr3bMXL", "title": "MXL population data (The 1000 Genomes Project)", "topics": [ ".Random.seed", "allGroups", "bamFiles", "copynumberGroups", "fcgr3bMXL", "objectCNVrd2", "readCountMatrix", "resultSegment" ] }, { "page": "groupBayesianCNVs", "title": "groupBayesianCNVs", "topics": [ "groupBayesianCNVs" ] }, { "page": "groupCNVs", "title": "Cluster segmentation scores into groups.", "topics": [ "groupCNVs" ] }, { "page": "groupCNVs-methods", "title": "Method 'groupCNVs'", "topics": [ "groupCNVs-methods" ] }, { "page": "identifyPolymorphicRegion", "title": "Identity polymorphic regions.", "topics": [ "identifyPolymorphicRegion" ] }, { "page": "identifyPolymorphicRegion-methods", "title": "Methods for Function 'identifyPolymorphicRegion'", "topics": [ "identifyPolymorphicRegion,CNVrd2-method", "identifyPolymorphicRegion-methods" ] }, { "page": "numericOrNULL-class", "title": "Class '\"numericOrNULL\"'", "topics": [ "numericOrNULL-class" ] }, { "page": "plotCNVrd2", "title": "Plot traces of samples.", "topics": [ "plotCNVrd2" ] }, { "page": "plotCNVrd2-methods", "title": "Method 'plotCNVrd2'", "topics": [ "plotCNVrd2-methods" ] }, { "page": "plotPolymorphicRegion", "title": "Plot polymorphic regions.", "topics": [ "plotPolymorphicRegion" ] }, { "page": "plotPolymorphicRegion-methods", "title": "Methods for Function 'plotPolymorphicRegion'", "topics": [ "plotPolymorphicRegion,CNVrd2-method", "plotPolymorphicRegion-methods" ] }, { "page": "searchGroupCNVs", "title": "Choose a number of CN groups", "topics": [ "searchGroupCNVs" ] }, { "page": "searchGroupCNVs-methods", "title": "Method 'searchGroupCNVs'", "topics": [ "searchGroupCNVs-methods" ] }, { "page": "segmentSamples", "title": "Implement the segmentation process", "topics": [ "segmentSamples" ] }, { "page": "segmentSamples-methods", "title": "Method 'segmentSamples'", "topics": [ "segmentSamples,CNVrd2-method", "segmentSamples-methods" ] }, { "page": "segmentSamplesUsingPopInformation", "title": "Implement the segmentation process for multiple populations", "topics": [ "segmentSamplesUsingPopInformation" ] }, { "page": "segmentSamplesUsingPopInformation-methods", "title": "Method 'segmentSamplesUsingPopInformation'", "topics": [ "segmentSamplesUsingPopInformation,CNVrd2-method", "segmentSamplesUsingPopInformation-methods" ] }, { "page": "vectorORfactor-class", "title": "Class '\"vectorORfactor\"'", "topics": [ "vectorORfactor-class" ] } ], "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "coda", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "DNAcopy", "farver", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "httr", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "RColorBrewer", "RCurl", "restfulr", "Rhtslib", "rjags", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "VariantAnnotation", "vctrs", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libjags", "package": "jags", "headers": "jags", "source": "jags", "version": "4.3.2-2.2404.0", "name": "jags", "homepage": "https://mcmc-jags.sourceforge.io", "description": "Just Another Gibbs Sampler for Bayesian MCMC - binary\nJAGS is Just Another Gibbs Sampler. It is a program for analysis of\nBayesian hierarchical models using Markov Chain Monte Carlo (MCMC)\nsimulation not wholly unlike BUGS.\n\nJAGS was written with three aims in mind:\n* To have an engine for the BUGS language that runs on Unix\n* To be extensible, allowing users to write their own functions,\ndistributions and samplers.\n* To be a plaftorm for experimentation with ideas in Bayesian modelling\n\nThis package contains the 'jags' binary as well as the associated\nshared library modules loaded by the binary." }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 3.9242792860618816, "_indexed": true, "_nocasepkg": "cnvrd2", "_universes": [ "bioc", "hoangtn" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.51.0", "date": "2026-05-30T10:00:39.000Z", "distro": "noble", "commit": "1e605d700f5051cb9e650c2ac47f38f482c5e37d", "fileid": "2b69263fdfc987f7d93da1320fa3f464a4b1238e9e93738cb80ecac0509e33d7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679596720" }, { "r": "4.6.0", "os": "linux", "version": "1.51.0", "date": "2026-05-30T10:01:26.000Z", "distro": "noble", "commit": "1e605d700f5051cb9e650c2ac47f38f482c5e37d", "fileid": "8c6af123350bd292c1c54ddc199dbbba559ba8ac8ce5f644825aca953aed25b5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679596720" }, { "r": "4.5.3", "os": "mac", "version": "1.51.0", "date": "2026-05-30T13:49:05.000Z", "commit": "1e605d700f5051cb9e650c2ac47f38f482c5e37d", "fileid": "d34de1e886b6ec4f38f7e4e236ba293b2da9943bffc2da5d2f3aa9ad16798798", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679596720" }, { "r": "4.6.0", "os": "mac", "version": "1.51.0", "date": "2026-05-30T13:49:31.000Z", "commit": "1e605d700f5051cb9e650c2ac47f38f482c5e37d", "fileid": "6f0144a965348060b971c38b94d25d0b6295fd3bafeb6c150a6d31f526d03faf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679596720" }, { "r": "4.6.0", "os": "wasm", "version": "1.51.0", "date": "2026-05-30T10:00:47.000Z", "commit": "1e605d700f5051cb9e650c2ac47f38f482c5e37d", "fileid": "4132a4470e6ceaa306d955f3b31ba52bd386e31648fcee89b204908b66f38bc9", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679596720" }, { "r": "4.7.0", "os": "win", "version": "1.51.0", "date": "2026-05-30T09:59:40.000Z", "commit": "1e605d700f5051cb9e650c2ac47f38f482c5e37d", "fileid": "163513c0d778b1167e622147a62807212035f21ca0f90c78893c8bcbb2bd93f0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679596720" }, { "r": "4.5.3", "os": "win", "version": "1.51.0", "date": "2026-05-30T09:59:56.000Z", "commit": "1e605d700f5051cb9e650c2ac47f38f482c5e37d", "fileid": "069f269af087d8ed8dffaad9a9cd1f9a6dd46eefd698ae2b8ba0ccf16710d168", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679596720" }, { "r": "4.6.0", "os": "win", "version": "1.51.0", "date": "2026-05-30T09:59:43.000Z", "commit": "1e605d700f5051cb9e650c2ac47f38f482c5e37d", "fileid": "eedc53279375b83da1d7f42fb89a8cb79f9e070355b97b4d5b2de2884aa07cfa", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679596720" } ] }