{ "_id": "6a1aeb4d1d7bb097a09f3c93", "Package": "LimROTS", "Title": "LimROTS: A Hybrid Method Integrating Empirical Bayes and\nReproducibility-Optimized Statistics for Robust Differential\nExpression Analysis", "Version": "1.5.0", "Authors@R": "c(person(given = \"Ali\", family = \"Mostafa Anwar\", role = c(\"aut\", \"cre\"),\nemail= \"aliali.mostafa99@gmail.com\",\ncomment = c(ORCID = \"0000-0002-5201-387X\")),\nperson(given = \"Leo\", family = \"Lahti\", role = c(\"aut\" ,\"ths\"),\nemail = \"leo.lahti@iki.fi\",\ncomment = c(ORCID = \"0000-0001-5537-637X\")),\nperson(given = \"Akewak\", family = \"Jeba\", role = c(\"aut\",\"ctb\"),\nemail = \"akewak.k.jeba@utu.fi\",\ncomment = c(ORCID = \"0009-0007-1347-7552\")),\nperson(given = \"Eleanor\", family = \"Coffey\", role = c(\"aut\", \"ths\"),\nemail = \"elecof@utu.fi\",\ncomment = c(ORCID = \"0000-0002-9717-5610\")),\nperson(given = \"Rasmus\", family = \"Hindström\", role = \"ctb\",\nemail = \"rasmus.hindstrom@utu.fi\",\ncomment = c(ORCID = \"0009-0004-5731-178X\")))", "Description": "Differential expression analysis is commonly used to study\ndiverse biological datasets. The reproducibility-optimized test\nstatistic (ROTS) (Elo et al., 2008,\n) uses a modified t-statistic to\nprioritise features that differ between two or more groups.\nHowever, the ROTS Bioconductor implementation (Suomi et al.,\n2017, ) did not accommodate\ntechnical or biological covariates. LimROTS (Anwar et al.,\n2025, ) addressed this\nlimitation by combining a reproducibility-optimized test\nstatistic with the limma empirical Bayes approach (Ritchie et\nal., 2015, ). This enables the analysis\nof more complex experimental designs and the incorporation of\ncovariates.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "biocViews": "Software, GeneExpression, DifferentialExpression,\nMicroarray, RNASeq, Proteomics, ImmunoOncology, Metabolomics,\nmRNAMicroarray", "URL": "https://github.com/AliYoussef96/LimROTS,\nhttps://aliyoussef96.github.io/LimROTS/", "BugReports": "https://github.com/AliYoussef96/LimROTS/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:04:05 UTC", "RemoteUrl": "https://github.com/bioc/LimROTS", "RemoteRef": "HEAD", "RemoteSha": "7309bb536a4e64e34902f4e8e68d67d495f33b75", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:39:29 UTC", "User": "root" }, "Author": "Ali Mostafa Anwar [aut, cre] (ORCID:\n),\nLeo Lahti [aut, ths] (ORCID: ),\nAkewak Jeba [aut, ctb] (ORCID: ),\nEleanor Coffey [aut, ths] (ORCID:\n),\nRasmus Hindström [ctb] (ORCID: )", "Maintainer": "Ali Mostafa Anwar ", "MD5sum": "613cab836e5b3032efb4825fc7cd9341", "_user": "bioc", "_type": "src", "_file": "LimROTS_1.5.0.tar.gz", "_fileid": "05c4e640f26905f795f8dde2fffaa537028c6ce1742bd729878157adc80b2001", "_filesize": 992414, "_sha256": "05c4e640f26905f795f8dde2fffaa537028c6ce1742bd729878157adc80b2001", "_created": "2026-05-30T09:39:29.000Z", "_published": "2026-05-30T13:51:09.065Z", "_jobs": [ { "job": 78640239082, "time": 223, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307369230" }, { "job": 78640239113, "time": 398, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307385660" }, { "job": 78640239125, "time": 524, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307396992" }, { "job": 78640239071, "time": 279, "config": "macos-oldrel-arm64", "r": 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