Pirat
This is the released version of Pirat; for the devel version, see Pirat.
Precursor or Peptide Imputation under Random Truncation
Bioconductor version: Release (3.23)
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("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 1.6.1, 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")
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 | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Preprocessing, Proteomics, Software |
| Version | 1.6.1 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | GPL-2 |
| Depends | R (>= 4.5.0) |
| Imports | basilisk, reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors |
| System Requirements | |
| URL | https://github.com/edyp-lab/Pirat |
| Bug Reports | https://github.com/edyp-lab/Pirat/issues |
See More
| Suggests | knitr, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Pirat_1.6.1.tar.gz |
| Windows Binary (x86_64) | Pirat_1.6.1.zip |
| macOS Binary (big-sur-x86_64) | Pirat_1.6.1.tgz |
| macOS Binary (sonoma-arm64) | Pirat_1.6.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Pirat |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Pirat |
| Package Short Url | https://bioconductor.org/packages/Pirat/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |