Package: MsQuality
Type: Package
Title: MsQuality - Quality metric calculation from Spectra and MsExperiment objects
Version: 1.11.0
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
git_url: https://git.bioconductor.org/packages/MsQuality
git_branch: devel
git_last_commit: 58f05c8
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
