MsQuality
This is the development version of MsQuality; for the stable release version, see MsQuality.
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
Bioconductor version: Development (3.21)
The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.
Author: Thomas Naake [aut, cre] (ORCID:
Maintainer: Thomas Naake <thomasnaake at googlemail.com>
citation("MsQuality")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("MsQuality")
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("MsQuality")| QC for metabolomics and proteomics data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Metabolomics, Proteomics, QualityControl, Software |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | BiocParallel(>= 1.32.0), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), msdata(>= 0.32.0), MsExperiment(>= 0.99.0), plotly (>= 4.9.4.1), ProtGenerics(>= 1.24.0), rlang (>= 1.1.1), rmzqc (>= 0.5.0), shiny (>= 1.6.0), shinydashboard (>= 0.7.1), Spectra(>= 1.13.2), stats (>= 4.2.0), stringr (>= 1.4.0), tibble (>= 3.1.4), tidyr (>= 1.1.3), utils (>= 4.2.0) |
| System Requirements | |
| URL | https://www.github.com/tnaake/MsQuality/ |
See More
| Suggests | BiocGenerics(>= 0.24.0), BiocStyle(>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), mzR(>= 2.32.0), rmarkdown (>= 2.7), S4Vectors(>= 0.29.17), testthat (>= 2.2.1) |
| 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 | MsQuality_1.7.0.tar.gz |
| Windows Binary (x86_64) | MsQuality_1.7.0.zip |
| macOS Binary (x86_64) | MsQuality_1.7.0.tgz |
| macOS Binary (arm64) | MsQuality_1.7.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MsQuality |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MsQuality |
| Bioc Package Browser | https://code.bioconductor.org/browse/MsQuality/ |
| Package Short Url | https://bioconductor.org/packages/MsQuality/ |
| Package Downloads Report | Download Stats |