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pulsedSilac

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Analysis of pulsed-SILAC quantitative proteomics data

Bioconductor version: Release (3.17)

This package provides several tools for pulsed-SILAC data analysis. Functions are provided to organize the data, calculate isotope ratios, isotope fractions, model protein turnover, compare turnover models, estimate cell growth and estimate isotope recycling. Several visualization tools are also included to do basic data exploration, quality control, condition comparison, individual model inspection and model comparison.

Author: Marc Pagès-Gallego, Tobias B. Dansen

Maintainer: Marc Pagès-Gallego <M.PagesGallego at umcutrecht.nl>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

BiocManager::install("pulsedSilac")

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

Documentation

Reference Manual PDF

Details

biocViews Proteomics, Software
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 years)
License GPL-3
Depends R (>= 3.6.0)
Imports robustbase, methods, R.utils, taRifx, S4Vectors, SummarizedExperiment, ggplot2, ggridges, stats, utils, UpSetR, cowplot, grid, MuMIn
Linking To
Suggests testthat (>= 2.1.0), knitr, rmarkdown, gridExtra
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/pulsedSilac
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pulsedSilac
Package Short Url https://bioconductor.org/packages/pulsedSilac/
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