Pirat
Precursor or Peptide Imputation under Random Truncation
Bioconductor version: 3.23 · Package version: 1.6.1
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 |
| Downloads rank | 322 |
| Source branch | RELEASE_3_23 |
| biocViews | MassSpectrometry, Preprocessing, Proteomics, Software |
Documentation
Download
Follow the 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 (arm64) | Pirat_1.6.1.tgz |
| macOS binary (x86_64) | Pirat_1.6.1.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: basilisk, reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors