{ "_id": "6a227067cd65a98ecbd48916", "Package": "RChASM", "Title": "Detection of Chromosomal Aneuploidies in Ancient DNA Studies", "Version": "1.0.1", "Authors@R": "c(\nperson(\ngiven = \"Adam B.\",\nfamily = \"Rohrlach\",\nemail = \"adam.rohrlach@adelaide.edu.au\",\nrole = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-4204-5018\")\n),\nperson(\ngiven = \"Jono\",\nfamily = \"Tuke\",\nemail = \"simon.tuke@adelaide.edu.au\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1688-8951\")\n),\nperson(\ngiven = \"Wolfgang\",\nfamily = \"Haak\",\nemail = \"wolfgang_haak@eva.mpg.de\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-2475-2007\")\n)\n)", "Description": "An R implementation of ChASM (Chromosomal Aneuploidy\nScreening Methodology): a statistically rigorous Bayesian\napproach for screening data sets for autosomal and sex\nchromosomal aneuploidies. This package takes as input the\nnumber of (deduplicated) reads mapping to chromosomes 1-22 and\nthe X and Y chromosomes, and models these using a\nDirichlet-multinomial distribution. From this, This package\nreturns posterior probabilities of sex chromosomal karyotypes\n(XX, XY, XXY, XYY, XXX and X) and full autosomal aneuploidies\n(trisomy 13, trisomy 18 and trisomy 21). This package also\nreturns two diagnostic statistics: (i) a posterior probability\naddressing whether contamination between XX and XY may explain\nthe observed sex chromosomal aneuploidy, and (ii) a chi-squared\nstatistic measuring whether the observed read counts are too\ndivergent from the underlying distribution (and may represent\nabnormal sequencing/quality issues).", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "LazyData": "true", "VignetteBuilder": "knitr", "URL": "https://jonotuke.github.io/RChASM/,\nhttps://github.com/jonotuke/RChASM", "BugReports": "https://github.com/jonotuke/RChASM/issues", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev make libicu-dev libpng-dev libuv1-dev\nlibx11-dev", "Repository": "https://jonotuke.r-universe.dev", "Date/Publication": "2026-04-30 20:38:48 UTC", "RemoteUrl": "https://github.com/jonotuke/rchasm", "RemoteRef": "HEAD", "RemoteSha": "6cf17e35826caaddf2ef62b6f0f16d9cc5966616", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 06:41:03 UTC", "User": "root" }, "Author": "Adam B. Rohrlach [aut, cph] (ORCID:\n),\nJono Tuke [aut, cre] (ORCID: ),\nWolfgang Haak [aut] (ORCID: )", "Maintainer": "Jono Tuke ", "MD5sum": "cb93a1c0303acd7ccfe606d40f7ee936", "_user": "jonotuke", "_type": "src", "_file": "RChASM_1.0.1.tar.gz", "_fileid": "48181be07c2b2579bf8589e76e50671ccfc806b9c3a72cc7720e4cd73d6bd487", "_filesize": 1052774, "_sha256": "48181be07c2b2579bf8589e76e50671ccfc806b9c3a72cc7720e4cd73d6bd487", "_created": "2026-06-05T06:41:03.000Z", "_published": "2026-06-05T06:44:55.710Z", "_distro": "noble", "_jobs": [ { "job": 79677506380, "time": 159, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7430453324" }, { "job": 79677506363, "time": 206, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7430463905" }, { "job": 79677506355, "time": 196, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7430454049" }, { "job": 79677506339, "time": 144, "config": "macos-release-arm64", "r": "4.6.0", "check": 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