{ "_id": "6a0f77f5acfb0bcc41c622d8", "Package": "polyRAD", "Version": "2.0.1", "Date": "2026-03-21", "Title": "Genotype Calling with Uncertainty from Sequencing Data in\nPolyploids and Diploids", "Authors@R": "c(person(\"Lindsay V.\", \"Clark\", email = \"Lindsay.Clark@seattlechildrens.org\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-3881-9252\")),\nperson(\"U.S. National Science Foundation\", role = \"fnd\"))", "Author": "Lindsay V. Clark [aut, cre]\n(), U.S. National\nScience Foundation [fnd]", "Maintainer": "Lindsay V. Clark ", "VignetteBuilder": "knitr, rmarkdown", "Description": "Read depth data from genotyping-by-sequencing (GBS) or\nrestriction site-associated DNA sequencing (RAD-seq) are\nimported and used to make Bayesian probability estimates of\ngenotypes in polyploids or diploids. The genotype\nprobabilities, posterior mean genotypes, or most probable\ngenotypes can then be exported for downstream analysis.\n'polyRAD' is described by Clark et al. (2019)\n, and the Hind/He statistic for\nmarker filtering is described by Clark et al. (2022)\n. A variant calling pipeline\nfor highly duplicated genomes is also included and is described\nby Clark et al. (2020, Version 1)\n.", "License": "GPL (>= 2)", "URL": "https://github.com/lvclark/polyRAD", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://lvclark.r-universe.dev", "Date/Publication": "2026-03-22 00:34:31 UTC", "RemoteUrl": "https://github.com/lvclark/polyRAD", "RemoteRef": "HEAD", "RemoteSha": "4408d65bfd59b2d643d26eb869339348be61b13e", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-21 05:59:27 UTC", "User": "root" }, "MD5sum": "06c4a41f4b9425caf62bb1a8e1357eae", "_user": "lvclark", "_type": "src", "_file": "polyRAD_2.0.1.tar.gz", "_fileid": "c2ca75d405241683866acb493f3f9ad524998dbf256a2256f01da59bcaab6053", "_filesize": 4378592, "_sha256": "c2ca75d405241683866acb493f3f9ad524998dbf256a2256f01da59bcaab6053", "_created": "2026-05-21T05:59:27.000Z", "_published": "2026-05-21T21:24:05.778Z", "_distro": "noble", "_jobs": [ { "job": 77271334041, "time": 226, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7128376678" }, { "job": 77271333988, "time": 253, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7128383047" }, { "job": 77271334223, "time": 251, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7128382615" }, { "job": 77271334028, "time": 256, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7128383884" }, { "job": 77271334185, "time": 144, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7128358041" }, { "job": 77271333938, "time": 293, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7128392153" }, { "job": 77271334080, "time": 133, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7128356007" }, { "job": 77271334078, "time": 287, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7128390778" }, { "job": 77271333396, "time": 309, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7128325747" }, { "job": 77271333395, "time": 202, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7147539861" }, { "job": 77271333978, "time": 246, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7128381675" }, { "job": 77271334088, "time": 189, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7128368516" }, { "job": 77271333967, "time": 176, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7128365841" } ], "_buildurl": "https://github.com/r-universe/lvclark/actions/runs/26208238815", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/lvclark/polyRAD", "_commit": { "id": "4408d65bfd59b2d643d26eb869339348be61b13e", "author": "Lindsay Clark ", "committer": "Lindsay Clark ", "message": "Prevent error about unregistered method\n", "time": 1774139671 }, "_maintainer": { "name": "Lindsay V. 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Lots of prior work in plant genetics, population genetics, and polyploidy.", "uuid": 13499688 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "fastmatch", "role": "Imports" }, { "package": "pcaMethods", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "rrBLUP", "role": "Suggests" }, { "package": "Rsamtools", "role": "Suggests" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "Biostrings", "role": "Suggests" }, { "package": "GenomicRanges", "role": "Suggests" }, { "package": "VariantAnnotation", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "S4Vectors", "role": "Suggests" }, { "package": "IRanges", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "GenomicFeatures", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "adegenet", "role": "Suggests" }, { "package": "txdbmaker", "role": "Suggests" }, { "package": "polymapR", "role": "Suggests" }, { "package": "BSgenome", "role": "Suggests" } ], "_owner": "lvclark", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-12", "n": 3 } ], "_tags": [ { "name": "v2.0.1", "date": "2026-03-22" } ], "_topics": [ "bioinformatics", "dna-sequencing", "genotype-likelihoods", "genotyping-by-sequencing", "hacktoberfest", "rad-seq", "rad-sequencing", "snp-genotyping", "cpp" ], "_stars": 33, "_contributors": [ { "user": "lvclark", "count": 715, "uuid": 13499688 }, { "user": "katrinleinweber", "count": 1, "uuid": 9948149 } ], "_userbio": { "uuid": 13499688, "type": "user", "name": "Lindsay Clark", "description": "Computational biologist at Seattle Children's. 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"page": "AddPloidyChiSq", "title": "Chi-Square Test on Genotype Likelihood Distributions", "topics": [ "AddPloidyChiSq", "AddPloidyChiSq.RADdata" ] }, { "page": "AddPloidyLikelihood", "title": "Likelihoods for Possible Ploidies Based on Genotype Distributions", "topics": [ "AddPloidyLikelihood", "AddPloidyLikelihood.RADdata" ] }, { "page": "CanDoGetWeightedMeanGeno", "title": "Check Whether 'GetWeightedMeanGenotypes' Can Be Run", "topics": [ "CanDoGetWeightedMeanGeno" ] }, { "page": "EstimateContaminationRate", "title": "Estimate Sample Contamination Using Blanks", "topics": [ "EstimateContaminationRate", "EstimateContaminationRate.RADdata" ] }, { "page": "ExamineGenotype", "title": "Plots to Examine Genotype Calling at a Single Taxon and Allele", "topics": [ "ExamineGenotype", "ExamineGenotype.RADdata" ] }, { "page": "exampleRAD", "title": "Miniature Datasets for Testing polyRAD Functions", "topics": [ "exampleRAD", "exampleRAD_mapping", "Msi01genes" ] }, { "page": "ExpectedHindHe", "title": "Simulate Data to Get Expected Distribution of Hind/He", "topics": [ "ExpectedHindHe", "ExpectedHindHeMapping", "SimAlleleDepth", "SimGenotypes", "SimGenotypesMapping" ] }, { "page": "ExportGAPIT", "title": "Export RADdata Object for Use by Other R Packages", "topics": [ "ExportGAPIT", "Export_adegenet_genind", "Export_GWASpoly", "Export_MAPpoly", "Export_polymapR", "Export_polymapR_probs", "Export_rrBLUP_Amat", "Export_rrBLUP_GWAS", "Export_Structure", "Export_TASSEL_Numeric" ] }, { "page": "GetLikelyGen", "title": "Output the Most Likely Genotype", "topics": [ "GetLikelyGen" ] }, { "page": "GetWeightedMeanGenotypes", "title": "Export Numeric Genotype Values from Posterior Probabilities", "topics": [ "GetProbableGenotypes", "GetProbableGenotypes.RADdata", "GetWeightedMeanGenotypes", "GetWeightedMeanGenotypes.RADdata" ] }, { "page": "HindHe", "title": "Identify Non-Mendelian Loci and Taxa that Deviate from Ploidy Expectations", "topics": [ "HindHe", "HindHe.RADdata", 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Parameters for Isolocus Sorting", "topics": [ "readProcessSamMulti" ] }, { "page": "readStacks", "title": "Import Read Depth from Stacks", "topics": [ "readStacks" ] }, { "page": "readTagDigger", "title": "Import Read Counts from TagDigger", "topics": [ "readTagDigger" ] }, { "page": "readTASSELGBSv2", "title": "Import Read Depth and Alignment from TASSEL GBS v2", "topics": [ "readTASSELGBSv2" ] }, { "page": "reverseComplement", "title": "Reverse Complement of DNA Sequence Stored as Character String", "topics": [ "reverseComplement", "reverseComplement,character-method" ] }, { "page": "SetBlankTaxa", "title": "Functions to Assign Taxa to Specific Roles", "topics": [ "GetBlankTaxa", "GetDonorParent", "GetRecurrentParent", "SetBlankTaxa", "SetDonorParent", "SetRecurrentParent" ] }, { "page": "StripDown", "title": "Remove Unneeded Slots to Conserve Memory", "topics": [ "StripDown", "StripDown.RADdata" ] }, { "page": "SubsetByLocus", "title": "Create RADdata Objects with a Subset of Loci", 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