pulsedSilac

DOI: 10.18129/B9.bioc.pulsedSilac  

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

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see pulsedSilac.

Analysis of pulsed-SILAC quantitative proteomics data

Bioconductor version: 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>

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

PDF		Reference Manual

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
LinkingTo
Suggests	testthat (>= 2.1.0), knitr, rmarkdown, gridExtra
SystemRequirements
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Build Report

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 [email protected]:packages/pulsedSilac
Package Short Url	https://bioconductor.org/packages/pulsedSilac/
Package Downloads Report	Download Stats