Package: MSstatsShiny
Type: Package
Title: MSstats GUI for Statistical Anaylsis of Proteomics Experiments
Version: 1.12.1
Description: MSstatsShiny is an R-Shiny graphical user interface (GUI)
        integrated with the R packages MSstats, MSstatsTMT, and
        MSstatsPTM. It provides a point and click end-to-end analysis
        pipeline applicable to a wide variety of experimental designs.
        These include data-dependedent acquisitions (DDA) which are
        label-free or tandem mass tag (TMT)-based, as well as DIA, SRM,
        and PRM acquisitions and those targeting post-translational
        modifications (PTMs). The application automatically saves users
        selections and builds an R script that recreates their
        analysis, supporting reproducible data analysis.
Authors@R: c(
    person("Devon", "Kohler", email = "kohler.d@northeastern.edu", role = c("aut")),
    person("Anthony", "Wu", email = "wu.anthon@northeastern.edu", role = c("aut", "cre")),
    person("Deril", "Raju", email = "raju.d@northeastern.edu", role = c("aut")),
    person("Maanasa", "Kaza", email = "maanasakaza@gmail.com", role = c("aut")),
    person("Cristina", "Pasi", email = "cristinapasi@gmail.com", role = c("aut")),
    person("Ting", "Huang", email = "thuang0703@gmail.com", role = c("aut")),
    person("Mateusz", "Staniak", email = "mateusz.staniak@math.uni.wroc.pl", role = c("aut")),
    person("Dhaval", "Mohandas", email = "dhavalmohandas@gmail.com", role = c("aut")),
    person("Eduard", "Sabido", email = "eduard.sabido@crg.cat", role = c("aut")),
    person("Meena", "Choi", email = "choi.meena@gene.com", role = c("aut")),
    person("Olga", "Vitek", email = "o.vitek@northeastern.edu", role = "aut"))
License: Artistic-2.0
Depends: R (>= 4.2)
Imports: shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly,
        data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM,
        MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid,
        utils, stats, htmltools, methods, tidyr, grDevices, graphics,
        mockery, MSstatsBioNet, shinydashboard, arrow, tools,
        MSstatsResponse
Suggests: rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0),
        shinytest2,
VignetteBuilder: knitr
biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software,
        ShinyApps, DifferentialExpression, OneChannel, TwoChannel,
        Normalization, QualityControl, GUI
BugReports: https://github.com/Vitek-Lab/MSstatsShiny/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make libicu-dev libxml2-dev libssl-dev
        python3 libzmq3-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-01-23 02:31:13 UTC
RemoteUrl: https://github.com/bioc/MSstatsShiny
RemoteRef: RELEASE_3_22
RemoteSha: 76a682a9b11705323f320e9e9017295290f5a952
NeedsCompilation: no
Packaged: 2026-01-23 04:44:37 UTC; root
Author: Devon Kohler [aut],
  Anthony Wu [aut, cre],
  Deril Raju [aut],
  Maanasa Kaza [aut],
  Cristina Pasi [aut],
  Ting Huang [aut],
  Mateusz Staniak [aut],
  Dhaval Mohandas [aut],
  Eduard Sabido [aut],
  Meena Choi [aut],
  Olga Vitek [aut]
Maintainer: Anthony Wu <wu.anthon@northeastern.edu>
Built: R 4.5.2; ; 2026-01-23 04:46:54 UTC; windows
