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Pirat

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 cea.fr>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Pirat")

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

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 PDF
NEWS Text

Details

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
System Requirements
URL http://www.prostar-proteomics.org/
Bug Reports https://github.com/prostarproteomics/Pirat/issues
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Suggests knitr, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Pirat_0.99.26.tar.gz
Windows Binary Pirat_0.99.25.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/Pirat
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Pirat
Bioc Package Browser https://code.bioconductor.org/browse/Pirat/
Package Short Url https://bioconductor.org/packages/Pirat/
Package Downloads Report Download Stats