Pirat

Precursor or Peptide Imputation under Random Truncation

Bioconductor version: Release (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")

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-vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	MassSpectrometry, Preprocessing, Proteomics, Software
Version	1.0.0
In Bioconductor since	BioC 3.20 (R-4.4) (< 6 months)
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

Suggests	knitr, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	Pirat_1.0.0.tar.gz
Windows Binary (x86_64)	Pirat_1.0.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)	Pirat_1.0.0.tgz
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