Package: MSstatsPTM
Type: Package
Title: Statistical Characterization of Post-translational Modifications
Version: 2.15.0
Date: 2024-11-25
Description: MSstatsPTM provides general statistical methods for
        quantitative characterization of post-translational
        modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass
        tag (TMT) labeling. Typically, the analysis involves the
        quantification of PTM sites (i.e., modified residues) and their
        corresponding proteins, as well as the integration of the
        quantification results. MSstatsPTM provides functions for
        summarization, estimation of PTM site abundance, and detection
        of changes in PTMs across experimental conditions.
Authors@R: c(
    person("Devon", "Kohler", email = "kohler.d@northeastern.edu", role = c("aut")),
    person("Tsung-Heng", "Tsai", email="tsai.tsungheng@gmail.com", role=c("aut")),
    person("Anthony", "Wu", email = "wu.anthon@northeastern.edu", role = c("aut", "cre")),
    person("Deril", "Raju", email = "raju.d@northeastern.edu", role = "aut"),
    person("Ting", "Huang", email = "thuang0703@gmail.com", role=c("aut")),
    person("Mateusz", "Staniak", email = "mtst@mstaniak.pl", role = c("aut")),
  	person("Meena", "Choi", email = "mnchoi67@gmail.com", role="aut"),
  	person("Olga", "Vitek", email = "o.vitek@northeastern.edu", role = "aut"))
License: Artistic-2.0
Depends: R (>= 4.3)
Imports: dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices,
        MSstatsTMT, MSstatsConvert (>= 1.19.1), MSstats, data.table,
        Rcpp, Biostrings, checkmate, ggrepel, plotly, htmltools, rlang
Suggests: knitr, rmarkdown, tinytest, covr, mockery, arrow, testthat
        (>= 3.0.0)
LazyData: true
LinkingTo: Rcpp
VignetteBuilder: knitr
biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software,
        DifferentialExpression, OneChannel, TwoChannel, Normalization,
        QualityControl
BugReports: https://github.com/Vitek-Lab/MSstatsPTM/issues
Encoding: UTF-8
URL: https://vitek-lab.github.io/MSstatsPTM/
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:53:49 UTC
RemoteUrl: https://github.com/bioc/MSstatsPTM
RemoteRef: HEAD
RemoteSha: 7d1f7035466cbd66969147bbed0cff66edcd60e5
NeedsCompilation: yes
Packaged: 2026-06-23 15:58:35 UTC; root
Author: Devon Kohler [aut],
  Tsung-Heng Tsai [aut],
  Anthony Wu [aut, cre],
  Deril Raju [aut],
  Ting Huang [aut],
  Mateusz Staniak [aut],
  Meena Choi [aut],
  Olga Vitek [aut]
Maintainer: Anthony Wu <wu.anthon@northeastern.edu>