Type: Package
Package: MSstatsLiP
Title: LiP Significance Analysis in shotgun mass spectrometry-based
        proteomic experiments
Version: 1.19.0
Date: 2024-3-19
Description: Tools for LiP peptide and protein significance analysis.
        Provides functions for summarization, estimation of LiP peptide
        abundance, and detection of changes across conditions. Utilizes
        functionality across the MSstats family of packages.
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("Tsung-Heng", "Tsai", email = "tsai.tsungheng@gmail.com", role = "aut"),
            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("Valentina", "Cappelletti", email = "valentina.cappelletti@imsb.biol.ethz.ch", role="aut"),
            person("Liliana", "Malinovska", email = "malinovska@imsb.biol.ethz.ch", role="aut"),
          	person("Olga", "Vitek", email = "o.vitek@northeastern.edu", role = "aut"))
License: Artistic-2.0
Depends: R (>= 4.1)
Imports: dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats,
        MSstatsConvert, data.table, Biostrings, MSstatsPTM (>= 2.12.0),
        Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr,
        tidyverse, scales, stats, plotly, htmltools
Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
LinkingTo: Rcpp
VignetteBuilder: knitr
biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software,
        DifferentialExpression, OneChannel, TwoChannel, Normalization,
        QualityControl
BugReports: https://github.com/Vitek-Lab/MSstatsLiP/issues
Encoding: UTF-8
LazyData: TRUE
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev make libharfbuzz-dev libicu-dev libjpeg-dev
        libpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev
        libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:57:16 UTC
RemoteUrl: https://github.com/bioc/MSstatsLiP
RemoteRef: HEAD
RemoteSha: 28c13fd171296fc12b2b396b1ab58a2d530218b2
NeedsCompilation: yes
Packaged: 2026-07-03 21:15:51 UTC; root
Author: Devon Kohler [aut],
  Anthony Wu [aut, cre],
  Tsung-Heng Tsai [aut],
  Deril Raju [aut],
  Ting Huang [aut],
  Mateusz Staniak [aut],
  Meena Choi [aut],
  Valentina Cappelletti [aut],
  Liliana Malinovska [aut],
  Olga Vitek [aut]
Maintainer: Anthony Wu <wu.anthon@northeastern.edu>