Package: limpa
Version: 1.3.3
Date: 2026-01-11
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 expression level of each peptide, and uses it to
        incorporate peptide missing values into protein quantification
        and into subsequent differential expression analyses. The
        package produces objects suitable for downstream analysis in
        limma. The package accepts feature-level data (fragments or
        precursors or peptides) 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 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: arrow, knitr, 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: 2026-01-11 09:06:54 UTC
RemoteUrl: https://github.com/bioc/limpa
RemoteRef: HEAD
RemoteSha: fc898d30907ad89c01b5b2e3468870ed7fb7a5e6
NeedsCompilation: no
Packaged: 2026-01-12 03:52:34 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>
Built: R 4.6.0; ; 2026-01-12 03:53:51 UTC; windows
