Package: limpa
Version: 1.5.0
Date: 2026-04-26
Title: Quantification and Differential Analysis of Proteomics Data
Description: Quantification and differential analysis of
        mass-spectrometry proteomics data, with probabilistic recovery
        of information from missing values. Avoids the need for
        imputation. Estimates the detection probability curve (DPC),
        which relates the probability of successful detection to the
        underlying log-intensity of each precursor ion, and uses it to
        incorporate missing values into protein quantification and into
        subsequent differential expression analyses. The package
        produces objects suitable for downstream analysis in limma. The
        package accepts precursor (or peptide) intensities including
        missing values and produces complete protein quantifications
        without the need for imputation. The uncertainty of the protein
        quantifications is propagated through to the limma analyses
        using variance modeling and precision weights, ensuring
        accurate error rate control. The analysis pipeline can
        alternatively work with PTM or protein level data. The package
        name "limpa" is an acronym for "Linear Models for Proteomics
        Data".
Authors@R: c(person("Mengbo", "Li",
  email = "li.me@wehi.edu.au",
  role = "aut",
  comment = c(ORCID = "0000-0002-9666-5810")),
  person("Pedro", "Baldoni",
  email = "baldoni.p@wehi.edu.au",
  role = "ctb",
  comment = c(ORCID = "0000-0002-9510-8326")),
  person("Gordon", "Smyth",
  email = "smyth@wehi.edu.au",
  role = c("cre", "aut"),
  comment = c(ORCID = "0000-0001-9221-2892")))
License: GPL (>=2)
Depends: limma
Imports: methods, stats, data.table, statmod
Suggests: knitr, nanoparquet, BiocStyle
VignetteBuilder: knitr
URL: https://github.com/SmythLab/limpa
biocViews: Bayesian, BiologicalQuestion, DataImport,
        DifferentialExpression, GeneExpression, MassSpectrometry,
        Preprocessing, Proteomics, Regression, Software
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:04:41 UTC
RemoteUrl: https://github.com/bioc/limpa
RemoteRef: HEAD
RemoteSha: 8edf301af1aa41dd8ddcd75355ee925cc76d1383
NeedsCompilation: no
Packaged: 2026-07-03 12:38:25 UTC; root
Author: Mengbo Li [aut] (ORCID: <https://orcid.org/0000-0002-9666-5810>),
  Pedro Baldoni [ctb] (ORCID: <https://orcid.org/0000-0002-9510-8326>),
  Gordon Smyth [cre, aut] (ORCID:
    <https://orcid.org/0000-0001-9221-2892>)
Maintainer: Gordon Smyth <smyth@wehi.edu.au>