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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: 0.99.10
doi: 10.1093/bioinformatics/btad200
abstract: 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:
- 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: 'Neither random nor censored: estimating intensity-dependent probabilities
    for missing values in label-free proteomics'
  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 K
  journal: Bioinformatics
  year: '2023'
  volume: '39'
  issue: '5'
  doi: 10.1093/bioinformatics/btad200
  start: btad200
repository: https://bioc.r-universe.dev
commit: daba68a28d0d141672aa90975c54ecfc04fffb17
date-released: '2025-03-25'
contact:
- family-names: Smyth
  given-names: Gordon
  email: smyth@wehi.edu.au
  orcid: https://orcid.org/0000-0001-9221-2892