pulsedSilac
This package is for version 3.11 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: 3.11
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("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 |
Details
| biocViews | Proteomics, Software |
| Version | 1.2.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | testthat (>= 2.1.0), knitr, rmarkdown, gridExtra |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pulsedSilac_1.2.0.tar.gz |
| Windows Binary | pulsedSilac_1.2.0.zip |
| macOS 10.13 (High Sierra) | pulsedSilac_1.2.0.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 3.11 | Source Archive |