pulsedSilac

DOI: 10.18129/B9.bioc.pulsedSilac    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see pulsedSilac.

Analysis of pulsed-SILAC quantitative proteomics data

Bioconductor version: 3.14

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 "4.1") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("pulsedSilac")

 

HTML	R Script	Pulsed-SILAC data analysis
PDF		Reference Manual

Details

biocViews	Proteomics, Software
Version	1.8.0
In Bioconductor since	BioC 3.10 (R-3.6) (2.5 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
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	pulsedSilac_1.8.0.tar.gz
Windows Binary	pulsedSilac_1.8.0.zip
macOS 10.13 (High Sierra)	pulsedSilac_1.8.0.tgz
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/
Package Downloads Report	Download Stats