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MQmetrics

Quality Control of Protemics Data


Bioconductor version: Release (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")

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 1.10.0
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, ggpubr, stats, cowplot, RColorBrewer, tidyr, scales, grid, rlang, ggforce, grDevices, gtable, plyr, knitr, rmarkdown, ggrepel, gghalves, tools
System Requirements
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Suggests testthat (>= 3.0.0), BiocStyle
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Build Report Build Report

Package Archives

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

Source Package MQmetrics_1.10.0.tar.gz
Windows Binary MQmetrics_1.10.0.zip
macOS Binary (x86_64) MQmetrics_1.10.0.tgz
macOS Binary (arm64) MQmetrics_1.10.0.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