Package: LimROTS
Title: LimROTS: A Hybrid Method Integrating Empirical Bayes and
        Reproducibility-Optimized Statistics for Robust Differential
        Expression Analysis
Version: 1.1.4
Authors@R: 
    c(person(given = "Ali", family = "Mostafa Anwar", role = c("aut", "cre"), 
    email= "aliali.mostafa99@gmail.com",
    comment = c(ORCID = "0000-0002-5201-387X")),
    person(given = "Leo", family = "Lahti", role = c("aut" ,"ths"),
    email = "leo.lahti@iki.fi",
    comment = c(ORCID = "0000-0001-5537-637X")),
    person(given = "Akewak", family = "Jeba", role = c("aut","ctb"),
    email = "akewak.k.jeba@utu.fi",
    comment = c(ORCID = "0009-0007-1347-7552")),
    person(given = "Eleanor", family = "Coffey", role = c("aut", "ths"),
    email = "elecof@utu.fi",
    comment = c(ORCID = "0000-0002-9717-5610")))
Description: 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.
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.5.0), SummarizedExperiment
biocViews: Software, GeneExpression, DifferentialExpression,
        Microarray, RNASeq, Proteomics, ImmunoOncology, Metabolomics,
        mRNAMicroarray
URL: https://github.com/AliYoussef96/LimROTS,
        https://aliyoussef96.github.io/LimROTS/
BugReports: https://github.com/AliYoussef96/LimROTS/issues
VignetteBuilder: knitr
Imports: limma, stringr, qvalue, utils, stats, BiocParallel, S4Vectors,
        dplyr
Suggests: BiocStyle, ggplot2, magick, testthat (>= 3.0.0), knitr,
        rmarkdown, caret, ROTS
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/LimROTS
git_branch: devel
git_last_commit: 24550a1
git_last_commit_date: 2025-06-16
Repository: Bioconductor 3.22
Date/Publication: 2025-06-16
NeedsCompilation: no
Packaged: 2025-06-16 23:59:31 UTC; biocbuild
Author: Ali Mostafa Anwar [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5201-387X>),
  Leo Lahti [aut, ths] (ORCID: <https://orcid.org/0000-0001-5537-637X>),
  Akewak Jeba [aut, ctb] (ORCID: <https://orcid.org/0009-0007-1347-7552>),
  Eleanor Coffey [aut, ths] (ORCID:
    <https://orcid.org/0000-0002-9717-5610>)
Maintainer: Ali Mostafa Anwar <aliali.mostafa99@gmail.com>
Built: R 4.5.0; ; 2025-06-17 13:21:05 UTC; windows
