MQmetrics
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MQmetrics.
Quality Control of Protemics Data
Bioconductor version: 3.13
The package MQmetrics (MaxQuant metrics) provides a workflow to analyze the quality and reproducibility of your proteomics mass spectrometry analysis from MaxQuant.Input data are extracted from several MaxQuant output tables, and produces a pdf report. It includes several visualization tools to check numerous parameters regarding the quality of the runs.It also includes two functions to visualize the iRT peptides from Biognosysin case they were spiked in the samples.
Author: Alvaro Sanchez-Villalba [aut, cre], Thomas Stehrer [aut], Marek Vrbacky [aut]
Maintainer: Alvaro Sanchez-Villalba <sanchezvillalba.alvaro at gmail.com>
citation("MQmetrics")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MQmetrics")
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("MQmetrics")| MQmetrics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| License | GPL-3 |
| Depends | |
| Imports | ggplot2, readr, magrittr, dplyr, purrr, reshape2, gridExtra, utils, stringr, chron, ggpubr, stats, cowplot, RColorBrewer, ggridges, tidyr, scales, grid, rlang, ggforce, grDevices, gtable, plyr, knitr, rmarkdown |
| System Requirements | |
| URL |
See More
| Suggests | testthat (>= 3.0.0) |
| 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 | MQmetrics_1.0.0.tar.gz |
| Windows Binary | MQmetrics_1.0.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | MQmetrics_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MQmetrics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MQmetrics |
| Bioc Package Browser | https://code.bioconductor.org/browse/MQmetrics/ |
| Package Short Url | https://bioconductor.org/packages/MQmetrics/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |