Package: MSstatsTMT
Title: Protein Significance Analysis in shotgun mass spectrometry-based
        proteomic experiments with tandem mass tag (TMT) labeling
Version: 2.18.0
Date: 2025-03-05
Description: The package provides statistical tools for detecting
        differentially abundant proteins in shotgun mass
        spectrometry-based proteomic experiments with tandem mass tag
        (TMT) labeling. It provides multiple functionalities, including
        aata visualization, protein quantification and normalization,
        and statistical modeling and inference. Furthermore, it is
        inter-operable with other data processing tools, such as
        Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.
Authors@R: c(person("Devon", "Kohler", email = "kohler.d@northeastern.edu", role=c("aut","cre")),
  person("Ting", "Huang", email = "thuang0703@gmail.com", role=c("aut")),
	person("Meena", "Choi", email = "mnchoi67@gmail.com", role="aut"),
	person("Mateusz", "Staniak", email = "mtst@mstaniak.pl", role = "aut"),
    	person("Tony", "Wu", email = "wu.anthon@northeastern.edu", role = "aut"),
    	person("Deril", "Raju", email = "raju.d@northeastern.edu", role = "aut"),
	person("Sicheng", "Hao", email = "hao.sic@husky.neu.edu", role = "aut"),
	person("Olga", "Vitek", email = "o.vitek@northeastern.edu", role = "aut"))
License: Artistic-2.0
Depends: R (>= 4.2)
Imports: limma, lme4, lmerTest, methods, data.table, stats, utils,
        ggplot2, grDevices, graphics, MSstats, MSstatsConvert,
        checkmate, plotly, htmltools
Suggests: BiocStyle, knitr, rmarkdown, testthat
VignetteBuilder: knitr
biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software
Encoding: UTF-8
LazyData: true
URL: http://msstats.org/msstatstmt/
BugReports: https://groups.google.com/forum/#!forum/msstats
RoxygenNote: 7.3.1
Config/pak/sysreqs: cmake make libicu-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:48:02 UTC
RemoteUrl: https://github.com/bioc/MSstatsTMT
RemoteRef: RELEASE_3_22
RemoteSha: ad356e06c0cf0d7956e0ab1cdb86835f1725adfd
NeedsCompilation: no
Packaged: 2026-01-30 20:39:52 UTC; root
Author: Devon Kohler [aut, cre],
  Ting Huang [aut],
  Meena Choi [aut],
  Mateusz Staniak [aut],
  Tony Wu [aut],
  Deril Raju [aut],
  Sicheng Hao [aut],
  Olga Vitek [aut]
Maintainer: Devon Kohler <kohler.d@northeastern.edu>
Built: R 4.5.2; ; 2026-01-30 20:42:29 UTC; windows
