pulsedSilac

This package is for version 3.12 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: 3.12

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 "4.0") 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")
Pulsed-SILAC data analysis HTML R Script
Reference Manual PDF

Details

biocViews Proteomics, Software
Version 1.4.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
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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 pulsedSilac_1.4.0.tar.gz
Windows Binary pulsedSilac_1.4.0.zip
macOS 10.13 (High Sierra) pulsedSilac_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pulsedSilac
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pulsedSilac
Bioc Package Browser https://code.bioconductor.org/browse/pulsedSilac/
Package Short Url https://bioconductor.org/packages/pulsedSilac/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive