Package: MsQuality
Type: Package
Title: MsQuality - Quality metric calculation from Spectra and
        MsExperiment objects
Version: 1.11.2
Date: 2025-03-02
Authors@R: c(person(given = "Thomas", family = "Naake",
		email = "thomasnaake@googlemail.com", role = c("aut", "cre"),
		comment = c(ORCID = "0000-0001-7917-5580")),
	person(given = "Johannes", family = "Rainer",
		email = "johannes.rainer@eurac.edu", role = "aut",
		comment = c(ORCID = "0000-0002-6977-7147")),
    person(given = "Helge", family = "Hecht",
          	email="helge.hecht@recetox.muni.cz", role="ctb"))
VignetteBuilder: knitr
Description: 
	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.
Depends: R (>= 4.2.0)
Imports: BiocParallel (>= 1.32.0), ggplot2 (>= 3.3.5), htmlwidgets (>=
        1.5.3), methods (>= 4.2.0), MsDataHub (>= 1.11.0), 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)
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)
biocViews: Metabolomics, Proteomics, MassSpectrometry, QualityControl
URL: https://www.github.com/tnaake/MsQuality/
BugReport: https://www.github.com/tnaake/MsQuality/issues/
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.3
git_url: https://git.bioconductor.org/packages/MsQuality
git_branch: devel
git_last_commit: f7b242d
git_last_commit_date: 2026-03-02
Repository: Bioconductor 3.23
Date/Publication: 2026-03-05
NeedsCompilation: no
Packaged: 2026-03-05 22:07:59 UTC; biocbuild
Author: Thomas Naake [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7917-5580>),
  Johannes Rainer [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>),
  Helge Hecht [ctb]
Maintainer: Thomas Naake <thomasnaake@googlemail.com>
Built: R 4.6.0; ; 2026-03-06 04:32:56 UTC; unix
