MQmetrics

This is the development version of MQmetrics; for the stable release version, see MQmetrics.

Quality Control of Protemics Data

Bioconductor version: Development (3.18)

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 Biognosys in 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 (from within R, enter citation("MQmetrics")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	PDF
NEWS	Text

Details

biocViews	DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version	1.9.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	GPL-3
Depends
Imports	ggplot2, readr, magrittr, dplyr, purrr, reshape2, gridExtra, utils, stringr, ggpubr, stats, cowplot, RColorBrewer, tidyr, scales, grid, rlang, ggforce, grDevices, gtable, plyr, knitr, rmarkdown, ggrepel, gghalves, tools
Linking To
Suggests	testthat (>= 3.0.0), BiocStyle
System Requirements
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	MQmetrics_1.9.0.tar.gz
Windows Binary	MQmetrics_1.9.0.zip
macOS Binary (x86_64)	MQmetrics_1.9.0.tgz
macOS Binary (arm64)	MQmetrics_1.9.0.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