Package: LimROTS
Title: LimROTS: A Hybrid Method Integrating Empirical Bayes and
        Reproducibility-Optimized Statistics for Robust Differential
        Expression Analysis
Version: 1.2.8
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: GPL (>= 2)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.4.0), 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
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-12-05 23:23:17 UTC
RemoteUrl: https://github.com/bioc/LimROTS
RemoteRef: RELEASE_3_22
RemoteSha: a28d957a0bd614c4b3296f295dd8699c9997144f
NeedsCompilation: no
Packaged: 2025-12-06 04:00:50 UTC; root
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 4.5.2; ; 2025-12-06 04:03:03 UTC; windows
