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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "limpa" in publications use:'
type: software
title: 'limpa: Quantification and Differential Analysis of Proteomics Data'
version: 1.4.0
doi: 10.1101/2025.04.28.651125
identifiers:
- type: doi
  value: 10.32614/CRAN.package.limpa
abstract: 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:
- family-names: Li
  given-names: Mengbo
  email: li.me@wehi.edu.au
  orcid: https://orcid.org/0000-0002-9666-5810
- family-names: Smyth
  given-names: Gordon
  email: smyth@wehi.edu.au
  orcid: https://orcid.org/0000-0001-9221-2892
preferred-citation:
  type: article
  title: Quantification and differential analysis of mass spectrometry proteomics
    data with probabilistic recovery of information from missing values
  authors:
  - family-names: Li
    given-names: Mengbo
    email: li.me@wehi.edu.au
    orcid: https://orcid.org/0000-0002-9666-5810
  - family-names: Cobbold
    given-names: Simon A
  - family-names: Smyth
    given-names: Gordon K
  journal: bioRxiv
  year: '2025'
  volume: April 29
  doi: 10.1101/2025.04.28.651125
  start: '651125'
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/SmythLab/limpa
commit: 8c409b3d2b5318afdd7213905feb03effc4f8774
url: https://github.com/SmythLab/limpa
date-released: '2026-04-26'
contact:
- family-names: Smyth
  given-names: Gordon
  email: smyth@wehi.edu.au
  orcid: https://orcid.org/0000-0001-9221-2892
references:
- type: article
  title: 'Neither random nor censored: estimating intensity-dependent probabilities
    for missing values in label-free proteomics'
  authors:
  - family-names: Li
    given-names: Mengbo
  - family-names: Smyth
    given-names: Gordon K
  journal: Bioinformatics
  year: '2023'
  volume: '39'
  issue: '5'
  doi: 10.1093/bioinformatics/btad200
  start: btad200