{ "_id": "6a17de17acfb0bcc41d9ced0", "Package": "LimROTS", "Title": "LimROTS: A Hybrid Method Integrating Empirical Bayes and\nReproducibility-Optimized Statistics for Robust Differential\nExpression Analysis", "Version": "1.4.0", "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, ). 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