# -------------------------------------------- # CITATION file created with {cffr} R package # See also: https://docs.ropensci.org/cffr/ # -------------------------------------------- cff-version: 1.2.0 message: 'To cite package "LimROTS" in publications use:' type: software license: GPL-2.0-or-later title: 'LimROTS: LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis' version: 1.4.0 doi: 10.1093/bioinformatics/btaf570 identifiers: - type: doi value: 10.32614/CRAN.package.LimROTS abstract: Differential expression analysis is commonly used to study diverse biological datasets. The reproducibility-optimized test statistic (ROTS) (Elo et al., 2008, ) uses a modified t-statistic to prioritise features that differ between two or more groups. However, the ROTS Bioconductor implementation (Suomi et al., 2017, ) did not accommodate technical or biological covariates. LimROTS (Anwar et al., 2025, ) addressed this limitation by combining a reproducibility-optimized test statistic with the limma empirical Bayes approach (Ritchie et al., 2015, ). This enables the analysis of more complex experimental designs and the incorporation of covariates. authors: - family-names: Mostafa Anwar given-names: Ali email: aliali.mostafa99@gmail.com orcid: https://orcid.org/0000-0002-5201-387X - family-names: Lahti given-names: Leo email: leo.lahti@iki.fi orcid: https://orcid.org/0000-0001-5537-637X - family-names: Jeba given-names: Akewak email: akewak.k.jeba@utu.fi orcid: https://orcid.org/0009-0007-1347-7552 - family-names: Coffey given-names: Eleanor email: elecof@utu.fi orcid: https://orcid.org/0000-0002-9717-5610 preferred-citation: type: article title: 'LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis' authors: - family-names: Anwar given-names: Ali Mostafa - family-names: Jeba given-names: Akewak email: akewak.k.jeba@utu.fi orcid: https://orcid.org/0009-0007-1347-7552 - family-names: Lahti given-names: Leo email: leo.lahti@iki.fi orcid: https://orcid.org/0000-0001-5537-637X - family-names: Coffey given-names: Eleanor email: elecof@utu.fi orcid: https://orcid.org/0000-0002-9717-5610 journal: Bioinformatics year: '2025' doi: 10.1093/bioinformatics/btaf570 notes: btaf570 repository: https://bioc-release.r-universe.dev repository-code: https://github.com/AliYoussef96/LimROTS commit: 85ad0edd0545ba7311f9bbf107213d43e9d93d4b url: https://aliyoussef96.github.io/LimROTS/ date-released: '2026-04-28' contact: - family-names: Mostafa Anwar given-names: Ali email: aliali.mostafa99@gmail.com orcid: https://orcid.org/0000-0002-5201-387X