MQmetrics

DOI: 10.18129/B9.bioc.MQmetrics    

Quality Control of Protemics Data

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!requireNamespace("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")

 

HTML R Script MQmetrics
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 1.2.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 years)
License GPL-3
Depends
Imports ggplot2, readr, magrittr, dplyr, purrr, reshape2, gridExtra, utils, stringr, ggpubr, stats, cowplot, RColorBrewer, ggridges, tidyr, scales, grid, rlang, ggforce, grDevices, gtable, plyr, knitr, rmarkdown, ggrepel, gghalves, tools
LinkingTo
Suggests testthat (>= 3.0.0), BiocStyle
SystemRequirements
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_1.2.0.tar.gz
Windows Binary MQmetrics_1.2.0.zip
macOS 10.13 (High Sierra) MQmetrics_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MQmetrics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MQmetrics
Package Short Url https://bioconductor.org/packages/MQmetrics/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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