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: 1.4.4
Authors@R: 
  c(person(given = "Lucas", 
          family = "Etourneau", 
          email = "lucas.etourneau@gmail.com", 
          role = c("cre", "aut"),
	  comment = c(ORCID = "0000-0002-8670-808X")),
    person(given = "Laura", 
          family = "Fancello", 
          email = " laura.fancello@cea.fr", 
          role = c("aut")),
    person(given = "Manon", 
          family = "Gaudin",
          email = "manon.gaudin@cea.fr",
          role = c("aut")),
    person(given = "Samuel", 
          family = "Wieczorek",
          email = "samuel.wieczorek@cea.fr",
          role = c("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)
Imports: basilisk, 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
Config/pak/sysreqs: libpng-dev python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-02-26 19:08:31 UTC
RemoteUrl: https://github.com/bioc/Pirat
RemoteRef: RELEASE_3_22
RemoteSha: f69c6f3572ee2c8da71edf3de5a55e229fb7a055
NeedsCompilation: no
Packaged: 2026-02-27 04:29:22 UTC; root
Author: Lucas Etourneau [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-8670-808X>),
  Laura Fancello [aut],
  Manon Gaudin [aut],
  Samuel Wieczorek [aut] (ORCID: <https://orcid.org/0000-0002-5016-1203>),
  Nelle Varoquaux [aut],
  Thomas Burger [aut]
Maintainer: Lucas Etourneau <lucas.etourneau@gmail.com>
Built: R 4.5.2; ; 2026-02-27 04:31:04 UTC; windows
