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This is the development version of Pirat; to use it, please install the devel version of Bioconductor.

Precursor or Peptide Imputation under Random Truncation

Bioconductor version: Development (3.20)

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 [aut], Laura Fancello [aut], Samuel Wieczorek [cre, aut] , Nelle Varoquaux [aut], Thomas Burger [aut]

Maintainer: Samuel Wieczorek <samuel.wieczorek at>

Citation (from within R, enter citation("Pirat")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Pirat HTML R Script
Reference Manual PDF


biocViews MassSpectrometry, Preprocessing, Proteomics, Software
Version 0.99.26
In Bioconductor since BioC 3.20 (R-4.4)
License GPL-2
Depends R (>= 4.4.0)
Imports basilisk, reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors
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Follow Installation instructions to use this package in your R session.

Source Package Pirat_0.99.26.tar.gz
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Source Repository (Developer Access) git clone
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