{ "_id": "6a1bfaac1d7bb097a0a27a93", "Package": "polysat", "Version": "1.7-8", "Date": "2024-12-20", "Title": "Tools for Polyploid Microsatellite Analysis", "Authors@R": "c(person(\"Lindsay V.\", \"Clark\", email = \"Lindsay.Clark@seattlechildrens.org\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-3881-9252\")),\nperson(\"Alistair J.\", \"Hall\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-9293-8909\")),\nperson(\"Handunnethi Nihal\", \"de Silva\", role = \"ctb\"),\nperson(\"Tyler William\", \"Smith\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-7683-2653\")))", "Description": "A collection of tools to handle microsatellite data of any\nploidy (and samples of mixed ploidy) where allele copy number\nis not known in partially heterozygous genotypes. It can\nimport and export data in ABI 'GeneMapper', 'Structure',\n'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi', 'POPDIST',\n'STRand', and binary presence/absence formats. It can\ncalculate pairwise distances between individuals using a\nstepwise mutation model or infinite alleles model, with or\nwithout taking ploidies and allele frequencies into account.\nThese distances can be used for the calculation of clonal\ndiversity statistics or used for further analysis in R. Allelic\ndiversity statistics and Polymorphic Information Content are\nalso available. polysat can assist the user in estimating the\nploidy of samples, and it can estimate allele frequencies in\npopulations, calculate pairwise or global differentiation\nstatistics based on those frequencies, and export allele\nfrequencies to 'SPAGeDi' and 'adegenet'. Functions are also\nincluded for assigning alleles to isoloci in cases where one\npair of microsatellite primers amplifies alleles from two or\nmore independently segregating isoloci. polysat is described by\nClark and Jasieniuk (2011)\n and Clark and Schreier\n(2017) .", "License": "GPL-2", "URL": "https://github.com/lvclark/polysat/wiki", "Repository": "https://lvclark.r-universe.dev", "Date/Publication": "2024-12-20 20:49:36 UTC", "RemoteUrl": "https://github.com/lvclark/polysat", "RemoteRef": "HEAD", "RemoteSha": "1bea7c88aa2b5da45fa74af6bcdf5e20faa68396", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-31 09:02:34 UTC", "User": "root" }, "Author": "Lindsay V. Clark [aut, cre] (ORCID:\n),\nAlistair J. Hall [ctb] (ORCID: ),\nHandunnethi Nihal de Silva [ctb],\nTyler William Smith [ctb] (ORCID:\n)", "Maintainer": "Lindsay V. Clark ", "MD5sum": "d327f8cfac5d91b24aca63882d9b6c04", "_user": "lvclark", "_type": "src", "_file": "polysat_1.7-8.tar.gz", "_fileid": "96082f6224014d3f49c869f469a47f6d4567788dc4e6a958cc4afe23fbea6231", "_filesize": 2345694, "_sha256": "96082f6224014d3f49c869f469a47f6d4567788dc4e6a958cc4afe23fbea6231", "_created": "2026-05-31T09:02:34.000Z", "_published": "2026-05-31T09:09:00.030Z", "_distro": "noble", "_jobs": [ { "job": 78713975753, "time": 141, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7315449881" }, { "job": 78713975758, "time": 199, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7315455846" }, { "job": 78713975756, "time": 163, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7315452374" }, { "job": 78713975764, "time": 149, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7315450746" }, { "job": 78713975785, "time": 248, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7315455949" }, { "job": 78713975749, "time": 341, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7315470216" }, { "job": 78713975752, "time": 168, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7315449845" }, { "job": 78713975762, "time": 324, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7315467833" }, { "job": 78713746891, "time": 225, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7315433998" }, { "job": 78713975699, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7315446656" }, { "job": 78713975744, "time": 126, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7315448236" }, { "job": 78713975743, "time": 120, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7315447798" }, { "job": 78713975750, "time": 137, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7315449499" } ], "_buildurl": "https://github.com/r-universe/lvclark/actions/runs/26708318268", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/lvclark/polysat", "_commit": { "id": "1bea7c88aa2b5da45fa74af6bcdf5e20faa68396", "author": "Lindsay Clark ", "committer": "Lindsay Clark ", "message": "Bug fix\n", "time": 1734727776 }, "_maintainer": { "name": "Lindsay V. Clark", "email": "lindsay.clark@seattlechildrens.org", "login": "lvclark", "orcid": "0000-0002-3881-9252", "description": "Computational biologist at Seattle Children's. Lots of prior work in plant genetics, population genetics, and polyploidy.", "uuid": 13499688 }, "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "ade4", "role": "Suggests" }, { "package": "adegenet", "role": "Suggests" }, { "package": "ape", "role": "Suggests" } ], "_owner": "lvclark", "_selfowned": true, "_usedby": 1, "_updates": [], "_tags": [], "_stars": 12, "_contributors": [ { "user": "lvclark", "count": 138, "uuid": 13499688 }, { "user": "plantarum", "count": 4, "uuid": 5727138 } ], "_userbio": { "uuid": 13499688, "type": "user", "name": "Lindsay Clark", "description": "Computational biologist at Seattle Children's. 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