MsQuality
This is the development version of MsQuality; for the stable release version, see MsQuality.
MsQuality - Quality metric calculation from Spectra, MsExperiment and Chromatograms objects
Bioconductor version: Development (3.23)
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. Additionally, MsQuality supports Chromatograms objects from the Chromatograms package for chromatographic quality metrics.
Author: Thomas Naake [aut, cre]
, Johannes Rainer [aut]
, Helge Hecht [ctb], Philippine Louail [aut]
Maintainer: Thomas Naake <thomasnaake at googlemail.com>
citation("MsQuality")):
Installation
To install this package, start R (version "4.6") 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 | 1.11.3 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | BiocParallel(>= 1.32.0), Chromatograms(>= 1.1.5), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), MsDataHub(>= 1.10.0), MsExperiment(>= 0.99.0), plotly (>= 4.9.4.1), ProtGenerics(>= 1.24.0), rlang (>= 1.1.1), rmzqc (>= 0.7.0), 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), MsCoreUtils(>= 1.19.0), MetaboCoreUtils(>= 1.19.2) |
| 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_1.11.3.tar.gz |
| Windows Binary (x86_64) | MsQuality_1.11.3.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | MsQuality_1.11.3.tgz |
| macOS Binary (big-sur-arm64) | MsQuality_1.11.2.tgz |
| macOS Binary (sonoma-arm64) | MsQuality_1.11.2.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 |