Package: MsQuality
Type: Package
Title: MsQuality - Quality metric calculation from Spectra and
        MsExperiment objects
Version: 1.10.0
Date: 2025-10-23
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")))
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), msdata (>= 0.32.0), 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: 7.3.2
Config/pak/sysreqs: libglpk-dev make libicu-dev libxml2-dev libssl-dev
        libnode-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:20:21 UTC
RemoteUrl: https://github.com/bioc/MsQuality
RemoteRef: RELEASE_3_22
RemoteSha: 04fa814e9d987ac17cf3ca6579199b69376124d3
NeedsCompilation: no
Packaged: 2026-01-27 08:57:12 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>)
Maintainer: Thomas Naake <thomasnaake@googlemail.com>
Built: R 4.5.2; ; 2026-01-27 08:59:46 UTC; windows
