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cff-version: 1.2.0
message: 'To cite package "LimROTS" in publications use:'
type: software
license: Artistic-2.0
title: 'LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized
  Statistics for Robust Analysis of Proteomics and Metabolomics Data'
version: 0.99.12
abstract: Differential expression analysis is a prevalent method utilised in the examination
  of diverse biological data. The reproducibility-optimized test statistic (ROTS)
  modifies a t-statistic based on the data's intrinsic characteristics and ranks features
  according to their statistical significance for differential expression between
  two or more groups (f-statistic). Focussing on proteomics and metabolomics, the
  current ROTS implementation cannot account for technical or biological covariates
  such as MS batches or gender differences among the samples. Consequently, we developed
  LimROTS, which employs a reproducibility-optimized test statistic utilising the
  limma methodology to simulate complex experimental designs. LimROTS is a hybrid
  method integrating empirical bayes and reproducibility-optimized statistics for
  robust analysis of proteomics and metabolomics data.
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
repository: https://bioc.r-universe.dev
repository-code: https://github.com/AliYoussef96/LimROTS
commit: aac524a0bde4bf7482a3324ea177e1edad0c5ebc
url: https://aliyoussef96.github.io/LimROTS/
contact:
- family-names: Mostafa Anwar
  given-names: Ali
  email: aliali.mostafa99@gmail.com
  orcid: https://orcid.org/0000-0002-5201-387X