Package: MsQuality
Type: Package
Title: MsQuality - Quality metric calculation from Spectra and
        MsExperiment objects
Version: 1.0.0
Date: 2023-04-18
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: ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>=
        4.2.0), MsExperiment (>= 0.99.0), plotly (>= 4.9.4.1),
        ProtGenerics (>= 1.24.0), shiny (>= 1.6.0), shinydashboard (>=
        0.7.1), Spectra (>= 1.2.0), stats (>= 4.2.0), stringr (>=
        1.4.0), tibble (>= 3.1.4), tidyr (>= 1.1.3), BiocParallel
Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>=
        1.0.5), knitr (>= 1.11), msdata (>= 0.32.0), 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: 7.2.3
git_url: https://git.bioconductor.org/packages/MsQuality
git_branch: RELEASE_3_17
git_last_commit: e4e396a
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
NeedsCompilation: no
Packaged: 2023-04-25 21:51:13 UTC; biocbuild
Author: Thomas Naake [aut, cre] (<https://orcid.org/0000-0001-7917-5580>),
  Johannes Rainer [aut] (<https://orcid.org/0000-0002-6977-7147>)
Maintainer: Thomas Naake <thomasnaake@googlemail.com>
Built: R 4.3.1; ; 2023-07-17 11:17:50 UTC; unix
