Pirat
Precursor or Peptide Imputation under Random Truncation
Bioconductor version: 3.24 · Package version: 1.7.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Pirat")Details
| Maintainer | Lucas Etourneau <lucas.etourneau@gmail.com> |
| Author | Lucas Etourneau [cre, aut] (ORCID: <https://orcid.org/0000-0002-8670-808X>), Laura Fancello [aut], Manon Gaudin [aut], Samuel Wieczorek [aut] (ORCID: <https://orcid.org/0000-0002-5016-1203>), Nelle Varoquaux [aut], Thomas Burger [aut] |
| License | GPL-2 |
| URL | https://github.com/edyp-lab/Pirat |
| Bug Reports | https://github.com/edyp-lab/Pirat/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | MassSpectrometry, Preprocessing, Proteomics, Software |
| Package Short Url | https://bioconductor.org/packages/Pirat/ |
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.
Documentation
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 |
Dependencies
Depends: R (>= 4.5.0)
Imports: basilisk, reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors
Reverse dependencies
Suggests Me (1): DaparToolshed