Package: MsQuality
Type: Package
Title: MsQuality - Quality metric calculation from Spectra,
        MsExperiment and Chromatograms objects
Version: 1.12.0
Date: 2026-03-30
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"),
	person(given = "Philippine", family = "Louail",
		email = "philippine.louail@outlook.com", role = "aut",
		comment = c(ORCID = "0009-0007-5429-6846")))
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. Additionally, MsQuality supports Chromatograms objects
	from the Chromatograms package for chromatographic quality metrics.
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)
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: RELEASE_3_23
git_last_commit: d37d179
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: no
Packaged: 2026-04-28 22:56:00 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],
  Philippine Louail [aut] (ORCID:
    <https://orcid.org/0009-0007-5429-6846>)
Maintainer: Thomas Naake <thomasnaake@googlemail.com>
Built: R 4.6.0; ; 2026-04-29 04:51:53 UTC; unix
