Package: limpa
Version: 1.3.1
Date: 2025-11-15
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. 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 peptide-level
        data with missing values and produces complete protein
        quantifications without missing values. The uncertainty
        introduced by missing value imputation is propagated through to
        the limma analyses using variance modeling and precision
        weights. 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: 2025-11-14 22:22:42 UTC
RemoteUrl: https://github.com/bioc/limpa
RemoteRef: HEAD
RemoteSha: 07af3cb7d6ecc780d049d9dc051ea1d25f792a84
NeedsCompilation: no
Packaged: 2025-11-15 03:34:41 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; ; 2025-11-15 03:36:14 UTC; windows
