{ "_id": "6a49430818cdde069385e968", "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": "2026-07-04 11:38:11 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 ", "_user": "bioc", "_type": "src", "_file": "LimROTS_1.5.0.tar.gz", "_fileid": "https://r2.ropensci.org/b534289537aba65754568b6196046d4700522194f8f31d8a9c5ab5b28e98c6b6", "_filesize": 996678, "_sha256": "b534289537aba65754568b6196046d4700522194f8f31d8a9c5ab5b28e98c6b6", "_expires": "2026-10-12T17:29:43.000Z", "_created": "2026-07-04T11:38:11.000Z", "_published": "2026-07-04T17:29:44.697Z", "_bioccheck": { "error": 0, "warning": 0, "note": 5 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28704844513", "_status": "success", "_upstream": "https://github.com/bioc/LimROTS", "_commit": { "id": "7309bb536a4e64e34902f4e8e68d67d495f33b75", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 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