Package: Pirat
Type: Package
Title: Precursor or Peptide Imputation under Random Truncation
Description: Pirat enables the imputation of missing values (either MNARs or 
  MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum 
  likelihood strategy. It does not require any parameter tuning, it models 
  the instrument censorship from the data available. It accounts for sibling
  peptides correlations and it can leverage complementary transcriptomics
  measurements. 
Version: 1.0.3
Authors@R: 
  c(person(given = "Lucas", 
          family = "Etourneau", 
          email = "lucas.etourneau@univ-grenoble-alpes.fr", 
          role = c("aut")),
    person(given = "Laura", 
          family = "Fancello", 
          email = " laura.fancello@cea.fr", 
          role = c("aut")),
    person(given = "Samuel", 
          family = "Wieczorek",
          email = "samuel.wieczorek@cea.fr",
          role = c("cre", "aut"),
          comment = c(ORCID="0000-0002-5016-1203")),
    person(given = "Nelle", 
          family = "Varoquaux",
          email = " nelle.varoquaux@univ-grenoble-alpes.fr",
          role = c("aut")),
    person(given = "Thomas", 
          family = "Burger",
          email = "thomas.burger@cea.fr",
          role = c("aut")))
License: GPL-2
Encoding: UTF-8
biocViews: Proteomics, MassSpectrometry, Preprocessing, Software
RoxygenNote: 7.3.2
BiocViews: Proteomics, MassSpectrometry
Depends: R (>= 4.4.0), BiocManager (>= 1.3.20)
Imports: basilisk (>= 1.18.0), reticulate, progress, ggplot2, MASS,
        invgamma, grDevices, stats, graphics, SummarizedExperiment,
        S4Vectors
Suggests: knitr, BiocStyle
VignetteBuilder: knitr
URL: https://github.com/edyp-lab/Pirat
BugReports: https://github.com/edyp-lab/Pirat/issues
StagedInstall: no
git_url: https://git.bioconductor.org/packages/Pirat
git_branch: RELEASE_3_20
git_last_commit: c6858d1
git_last_commit_date: 2025-03-03
Repository: Bioconductor 3.20
Date/Publication: 2025-03-03
NeedsCompilation: no
Packaged: 2025-03-04 02:16:08 UTC; biocbuild
Author: Lucas Etourneau [aut],
  Laura Fancello [aut],
  Samuel Wieczorek [cre, aut] (<https://orcid.org/0000-0002-5016-1203>),
  Nelle Varoquaux [aut],
  Thomas Burger [aut]
Maintainer: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Built: R 4.4.2; ; 2025-03-04 14:13:58 UTC; windows
