Pirat
This is the development version of Pirat; for the stable release version, see Pirat.
All Bioconductor versions of Pirat
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20
Precursor or Peptide Imputation under Random Truncation
Bioconductor version: 3.24 · Package version: 1.7.0
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.
Author: Lucas Etourneau [cre, aut] 
, Laura Fancello [aut], Manon Gaudin [aut], Samuel Wieczorek [aut] , Nelle Varoquaux [aut], Thomas Burger [aut]
Maintainer: Lucas Etourneau <lucas.etourneau at gmail.com>
Citation
From within R, enter citation("Pirat"):
Lucas Etourneau, Laura Fancello, Manon Gaudin, Samuel Wieczorek, Nelle Varoquaux, Thomas Burger. Pirat: Precursor or Peptide Imputation under Random Truncation. doi:10.18129/B9.bioc.Pirat, R package version 1.7.0, https://bioconductor.org/packages/Pirat.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("Pirat")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.7.0 |
| License | GPL-2 |
| URL | https://github.com/edyp-lab/Pirat |
| Bug Reports | https://github.com/edyp-lab/Pirat/issues |
| Last updated | 2026-08-12 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| Downloads rank | 1982 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | MassSpectrometry, Preprocessing, Proteomics, Software |
| Package Short Url | https://bioconductor.org/packages/Pirat/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Pirat")| Pirat | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | Pirat_1.7.0.tar.gz |
| Windows binary (x86_64) | Pirat_1.7.0.zip |
| macOS binary (arm64) | Pirat_1.7.0.tgz |
| macOS binary (x86_64) | Pirat_1.7.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Pirat |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Pirat |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: basilisk, reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors
Reverse dependencies
Suggests Me (1): DaparToolshed