Package: MsQuality
Type: Package
Title: MsQuality - Quality metric calculation from Spectra,
        MsExperiment and Chromatograms objects
Version: 1.13.0
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
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev libnode-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:59:32 UTC
RemoteUrl: https://github.com/bioc/MsQuality
RemoteRef: HEAD
RemoteSha: 342c9d67b512ae93e49d8e0e27b3654b33a25295
NeedsCompilation: no
Packaged: 2026-07-03 23:09:05 UTC; root
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>