{ "_id": "6a4a36d1ebd24c9589270c14", "Package": "PureCN", "Type": "Package", "Title": "Copy number calling and SNV classification using targeted short\nread sequencing", "Version": "2.19.0", "Date": "2026-02-17", "Authors@R": "c(person(\"Markus\", \"Riester\",\nrole = c(\"aut\", \"cre\"),\nemail = \"markus.riester@gmail.com\",\ncomment = c(ORCID = \"0000-0002-4759-8332\")),\nperson(\"Angad P.\", \"Singh\", role = \"aut\"))", "Description": "This package estimates tumor purity, copy number, and loss\nof heterozygosity (LOH), and classifies single nucleotide\nvariants (SNVs) by somatic status and clonality. PureCN is\ndesigned for targeted short read sequencing data, integrates\nwell with standard somatic variant detection and copy number\npipelines, and has support for tumor samples without matching\nnormal samples.", "VignetteBuilder": "knitr", "License": "Artistic-2.0", "BugReports": "https://github.com/lima1/PureCN/issues", "URL": "https://github.com/lima1/PureCN", "biocViews": "CopyNumberVariation, Software, Sequencing,\nVariantAnnotation, VariantDetection, Coverage, ImmunoOncology", "NeedsCompilation": "no", "ByteCompile": "yes", "RoxygenNote": "7.3.1", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:43:25 UTC", "RemoteUrl": "https://github.com/bioc/PureCN", "RemoteRef": "HEAD", "RemoteSha": "3bf84d2b077f90ccea86a7e2157828d2277c0e0d", "Packaged": { "Date": "2026-07-05 10:30:31 UTC", "User": "root" }, "Author": "Markus Riester [aut, cre] (ORCID:\n),\nAngad P. Singh [aut]", "Maintainer": "Markus Riester ", "_user": "bioc", "_type": "src", "_file": "PureCN_2.19.0.tar.gz", "_fileid": "https://r2.ropensci.org/65ca0f37394a7c03ffaed8770a228f9777020899d981e48cf7a5b20d1b11697a", "_filesize": 3464740, "_sha256": "65ca0f37394a7c03ffaed8770a228f9777020899d981e48cf7a5b20d1b11697a", "_expires": "2026-10-13T10:49:52.000Z", "_created": "2026-07-05T10:30:31.000Z", "_published": "2026-07-05T10:49:53.833Z", "_bioccheck": { "error": 0, "warning": 4, "note": 14 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28736430097", "_status": "failure", "_upstream": "https://github.com/bioc/PureCN", "_commit": { "id": "3bf84d2b077f90ccea86a7e2157828d2277c0e0d", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380205 }, "_maintainer": { "name": "Markus Riester", "email": "markus.riester@gmail.com", "orcid": "0000-0002-4759-8332" }, "_distro": "resolute", "_jobs": [ { "job": 85215040207, "time": 299, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8090919356" }, { "job": 85215040199, "time": 936, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8090993558" }, { "job": 85215040223, "time": 946, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8090994994" }, { "job": 85215040201, "time": 555, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8090947706" }, { "job": 85215040196, "time": 520, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8090943747" }, { "job": 85211356571, "time": 3339, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "8090885619" }, { "job": 85215040204, "time": 220, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8090910715" }, { "job": 85215040206, "time": 975, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8090998491" }, { "job": 85215040216, "time": 1080, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8091011750" }, { "job": 85215040208, "time": 860, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8090984258" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "DNAcopy", "role": "Depends" }, { "package": "VariantAnnotation", "version": ">= 1.14.1", "role": "Depends" }, { "package": "GenomicRanges", "version": ">= 1.20.3", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.2.1", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "futile.logger", "role": "Imports" }, { "package": "VGAM", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "mclust", "role": "Imports" }, { "package": "rhdf5", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "BiocParallel", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "PSCBS", "role": "Suggests" }, { "package": "R.utils", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "optparse", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "genomicsdb", "version": ">= 0.0.3", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-28", "n": 1 }, { "week": "2025-35", "n": 1 }, { "week": "2026-08", "n": 3 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.19.0", "bioc": "3.24" }, { "branch": "release", "version": "2.18.0", "bioc": "3.23" } ], "_topics": [ "copynumbervariation", "software", "sequencing", "variantannotation", "variantdetection", "coverage", "immunooncology", "bioconductor-package", "cell-free-dna", "copy-number", "loh", "tumor-heterogeneity", "tumor-mutational-burden", "tumor-purity" ], "_stars": 148, "_contributors": [ { "user": "lima1", "count": 1253, "uuid": 364466 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "andrewrech", "count": 4, "uuid": 10691207 }, { "user": "dtenenba", "count": 4, "uuid": 2286826 }, { "user": "hpages", "count": 4, "uuid": 8810451 }, { "user": "chapmanb", "count": 2, "uuid": 39391 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "ddrichel", "count": 1, "uuid": 15612230 }, { "user": "link-ny", "count": 1, "uuid": 4392950 }, { "user": "lbeltrame", "count": 1, "uuid": 25192 }, { "user": "nspies-carisls", "count": 1, "uuid": 156699954 }, { "user": "aoles", "count": 1, "uuid": 6545356 }, { "user": "lshep", "count": 1, "uuid": 18724380 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 11, "_devurl": "https://github.com/lima1/purecn", "_searchresults": 61, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PureCN.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/lima1/purecn", "_realowner": "bioc", "_cranurl": false, "_exports": [ "adjustLogRatio", "annotateTargets", "bootstrapResults", "calculateBamCoverageByInterval", "calculateLogRatio", "calculateMappingBiasGatk4", "calculateMappingBiasVcf", "calculatePowerDetectSomatic", "calculateTangentNormal", "callAlterations", "callAlterationsFromSegmentation", "callAmplificationsInLowPurity", "callCIN", "callLOH", "callMutationBurden", "correctCoverageBias", "createCurationFile", "createNormalDatabase", "filterIntervals", "filterVcfBasic", "filterVcfMuTect", "filterVcfMuTect2", "findFocal", "findHighQualitySNPs", "getSexFromCoverage", "getSexFromVcf", "plotAbs", "poolCoverage", "predictSomatic", "preprocessIntervals", "processMultipleSamples", "readAllelicCountsFile", "readCoverageFile", "readCurationFile", "readIntervalFile", "readLogRatioFile", "readSegmentationFile", "runAbsoluteCN", "segmentationCBS", "segmentationGATK4", "segmentationHclust", "segmentationPSCBS", "setMappingBiasVcf", "setPriorVcf" ], "_datasets": [ { "name": "centromeres", "title": "A list of data.frames containing centromere positions.", "object": "centromeres", "file": "centromeres.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "purecn.DNAcopy.bdry", "title": "DNAcopy boundary data", "object": "purecn.DNAcopy.bdry", "file": "purecn.DNAcopy.bdry.rda", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "purecn.example.output", "title": "Example output", "object": "purecn.example.output", "file": "purecn.example.output.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "adjustLogRatio", "title": "Adjust tumor vs. normal coverage log ratio for tumor purity and ploidy", "topics": [ "adjustLogRatio" ] }, { "page": "annotateTargets", "title": "Annotate targets with gene symbols", "topics": [ "annotateTargets" ] }, { "page": "bootstrapResults", "title": "Bootstrapping variant fits", "topics": [ "bootstrapResults" ] }, { "page": "calculateBamCoverageByInterval", "title": "Function to calculate coverage from BAM file", "topics": [ "calculateBamCoverageByInterval" ] }, { "page": "calculateLogRatio", "title": "Calculate coverage log-ratio of tumor vs. normal", "topics": [ "calculateLogRatio" ] }, { "page": "calculateMappingBiasGatk4", "title": "Calculate Mapping Bias from GATK4 GenomicsDB", "topics": [ "calculateMappingBiasGatk4" ] }, { "page": "calculateMappingBiasVcf", "title": "Calculate Mapping Bias", "topics": [ "calculateMappingBiasVcf" ] }, { "page": "calculatePowerDetectSomatic", "title": "Power calculation for detecting somatic mutations", "topics": [ "calculatePowerDetectSomatic" ] }, { "page": "calculateTangentNormal", "title": "Calculate tangent normal", "topics": [ "calculateTangentNormal" ] }, { "page": "callAlterations", "title": "Calling of amplifications and deletions", "topics": [ "callAlterations" ] }, { "page": "callAlterationsFromSegmentation", "title": "Calling of amplifications and deletions from segmentations", "topics": [ "callAlterationsFromSegmentation" ] }, { "page": "callAmplificationsInLowPurity", "title": "Calling of amplifications in low purity samples", "topics": [ "callAmplificationsInLowPurity" ] }, { "page": "callCIN", "title": "Call Chromosomal Instability", "topics": [ "callCIN" ] }, { "page": "callLOH", "title": "Get regions of LOH", "topics": [ "callLOH" ] }, { "page": "callMutationBurden", "title": "Call mutation burden", "topics": [ "callMutationBurden" ] }, { "page": "centromeres", "title": "A list of data.frames containing centromere positions.", "topics": [ "centromeres" ] }, { "page": "correctCoverageBias", "title": "Correct for library-specific coverage biases", "topics": [ "correctCoverageBias" ] }, { "page": "createCurationFile", "title": "Create file to curate PureCN results", "topics": [ "createCurationFile" ] }, { "page": "createNormalDatabase", "title": "Create database of normal samples", "topics": [ "createNormalDatabase" ] }, { "page": "filterIntervals", "title": "Remove low quality intervals", "topics": [ "filterIntervals" ] }, { "page": "filterVcfBasic", "title": "Basic VCF filter function", "topics": [ "filterVcfBasic" ] }, { "page": "filterVcfMuTect", "title": "Filter VCF MuTect", "topics": [ "filterVcfMuTect" ] }, { "page": "filterVcfMuTect2", "title": "Filter VCF MuTect2", "topics": [ "filterVcfMuTect2" ] }, { "page": "findFocal", "title": "Find focal amplifications", "topics": [ "findFocal" ] }, { "page": "findHighQualitySNPs", "title": "Find High Quality SNPs", "topics": [ "findHighQualitySNPs" ] }, { "page": "getSexFromCoverage", "title": "Get sample sex from coverage", "topics": [ "getSexFromCoverage" ] }, { "page": "getSexFromVcf", "title": "Get sample sex from a VCF file", "topics": [ "getSexFromVcf" ] }, { "page": "plotAbs", "title": "Plots for analyzing PureCN solutions", "topics": [ "plotAbs" ] }, { "page": "poolCoverage", "title": "Pool coverage from multiple samples", "topics": [ "poolCoverage" ] }, { "page": "predictSomatic", "title": "Predict germline vs. somatic status", "topics": [ "predictSomatic" ] }, { "page": "preprocessIntervals", "title": "Preprocess intervals", "topics": [ "preprocessIntervals" ] }, { "page": "processMultipleSamples", "title": "Multi sample normalization and segmentation", "topics": [ "processMultipleSamples" ] }, { "page": "PureCN-defunct", "title": "Defunct functions in package 'PureCN'", "topics": [ "PureCN-defunct" ] }, { "page": "PureCN-deprecated", "title": "Deprecated functions in package 'PureCN'", "topics": [ "PureCN-deprecated" ] }, { "page": "purecn.DNAcopy.bdry", "title": "DNAcopy boundary data", "topics": [ "purecn.DNAcopy.bdry" ] }, { "page": "purecn.example.output", "title": "Example output", "topics": [ "purecn.example.output" ] }, { "page": "readAllelicCountsFile", "title": "Read allelic counts file", "topics": [ "readAllelicCountsFile" ] }, { "page": "readCoverageFile", "title": "Read coverage file", "topics": [ "readCoverageFile" ] }, { "page": "readCurationFile", "title": "Read curation file", "topics": [ "readCurationFile" ] }, { "page": "readIntervalFile", "title": "Read interval file", "topics": [ "readIntervalFile" ] }, { "page": "readLogRatioFile", "title": "Read file containing interval-level log2 tumor/normal ratios", "topics": [ "readLogRatioFile" ] }, { "page": "readSegmentationFile", "title": "Read file containing segmentations", "topics": [ "readSegmentationFile" ] }, { "page": "runAbsoluteCN", "title": "Run PureCN implementation of ABSOLUTE", "topics": [ "runAbsoluteCN" ] }, { "page": "segmentationCBS", "title": "CBS segmentation", "topics": [ "segmentationCBS" ] }, { "page": "segmentationGATK4", "title": "GATK4 ModelSegments segmentation function", "topics": [ "segmentationGATK4" ] }, { "page": "segmentationHclust", "title": "Minimal segmentation function", "topics": [ "segmentationHclust" ] }, { "page": "segmentationPSCBS", "title": "PSCBS segmentation", "topics": [ "segmentationPSCBS" ] }, { "page": "setMappingBiasVcf", "title": "Set Mapping Bias VCF", "topics": [ "setMappingBiasVcf" ] }, { "page": "setPriorVcf", "title": "Set Somatic Prior VCF", "topics": [ "setPriorVcf" ] } ], "_readme": "https://github.com/bioc/PureCN/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "biocmake", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "dir.expiry", "DNAcopy", "farver", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "httr", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "RColorBrewer", "RCurl", "restfulr", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "UCSC.utils", "VariantAnnotation", "vctrs", "VGAM", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_score": 8.370564898376543, "_indexed": true, "_nocasepkg": "purecn", "_universes": [ "bioc", "lima1" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.19.0", "date": "2026-07-05T10:36:03.000Z", "distro": "resolute", "commit": "3bf84d2b077f90ccea86a7e2157828d2277c0e0d", "fileid": "https://r2.ropensci.org/5804361b7378cdac3f46747326a07ac9022c303c9d43c6dcd224b646278909f9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28736430097" }, { "r": "4.6.1", "os": "linux", "version": "2.19.0", "date": "2026-07-05T10:36:20.000Z", "distro": "resolute", "commit": "3bf84d2b077f90ccea86a7e2157828d2277c0e0d", "fileid": "https://r2.ropensci.org/773c335be9360f5457a6fc61bf4140b51592e510184ad09a896f4acdb69a5f04", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28736430097" }, { "r": "4.5.3", "os": "mac", "version": "2.19.0", "date": "2026-07-05T10:33:40.000Z", "commit": "3bf84d2b077f90ccea86a7e2157828d2277c0e0d", "fileid": "https://r2.ropensci.org/69ad096b38401e045b15d73477bc2e6a2c17f51251db018f1d9c4555e21e683f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28736430097" }, { "r": "4.6.1", "os": "mac", "version": "2.19.0", "date": "2026-07-05T10:33:41.000Z", "commit": "3bf84d2b077f90ccea86a7e2157828d2277c0e0d", "fileid": "https://r2.ropensci.org/fe1ab728530858633fd00c29073c3e160ac2e1e7b9333a89071e20e737c2b3d9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28736430097" }, { "r": "4.6.0", "os": "wasm", "version": "2.19.0", "date": "2026-07-05T10:35:04.000Z", "commit": "3bf84d2b077f90ccea86a7e2157828d2277c0e0d", "fileid": "https://r2.ropensci.org/3dd50ccd054bf1ce75fa543a3a53eddfaca0e9ae8e9095d672bcaf0b5206a8e2", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28736430097" }, { "r": "4.7.0", "os": "win", "version": "2.19.0", "date": "2026-07-05T10:34:06.000Z", "commit": "3bf84d2b077f90ccea86a7e2157828d2277c0e0d", "fileid": "https://r2.ropensci.org/0719a939b91fb701f5e5e8cd4268d41bce04808d0c0bc37a1843e8cf6f610142", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28736430097" }, { "r": "4.5.3", "os": "win", "version": "2.19.0", "date": "2026-07-05T10:34:08.000Z", "commit": "3bf84d2b077f90ccea86a7e2157828d2277c0e0d", "fileid": "https://r2.ropensci.org/b59e72f45ee40aeb2b52d8d065e9e628f46a71f00db186ac0fd125fd4a59ce66", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28736430097" }, { "r": "4.6.1", "os": "win", "version": "2.19.0", "date": "2026-07-05T10:34:38.000Z", "commit": "3bf84d2b077f90ccea86a7e2157828d2277c0e0d", "fileid": "https://r2.ropensci.org/0f65456b1ec57c8a9024fe15ad3409e238f6516e04c7ee7e1007a9d36ca53b75", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28736430097" } ] }