Package: DEP
Title: Differential Enrichment analysis of Proteomics data
Version: 3.99.0
Authors@R: c(
    person("Jelmer", "Dijkstra", email = "protechrobioMV@gmail.com", role = c("aut", "cre")),
    person("Arne", "Smits", email = "smits.arne@gmail.com", role = "aut"),
    person("Wolfgang", "Huber", email = "wolfgang.huber@embl.de", role = "aut"))
Description: This package provides an integrated analysis workflow for
        robust and reproducible analysis of mass spectrometry
        proteomics data for differential protein expression or
        differential enrichment. It requires tabular input (e.g. txt
        files) as generated by quantitative analysis softwares of raw
        mass spectrometry data, such as MaxQuant or IsobarQuant.
        Functions are provided for data preparation, filtering,
        variance normalization and imputation of missing values, as
        well as statistical testing of differentially enriched /
        expressed proteins. It also includes tools to check
        intermediate steps in the workflow, such as normalization and
        missing values imputation. Finally, visualization tools are
        provided to explore the results, including heatmap, volcano
        plot and barplot representations. For scientists with limited
        experience in R, the package also contains wrapper functions
        that entail the complete analysis workflow and generate a
        report. Even easier to use are the interactive Shiny apps that
        are provided by the package.
License: Artistic-2.0
Depends: R (>= 4.5.0)
Encoding: UTF-8
LazyData: true
Imports: ggplot2, dplyr, purrr, readr, tibble, tidyr,
        SummarizedExperiment (>= 1.11.5), MSnbase, limma, vsn, fdrtool,
        ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny,
        shinydashboard, DT, rmarkdown, assertthat, gridExtra, grid,
        stats, imputeLCMD, cluster
Suggests: testthat, enrichR, knitr, BiocStyle
biocViews: ImmunoOncology, Proteomics, MassSpectrometry,
        DifferentialExpression, DataRepresentation
VignetteBuilder: knitr
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libnetcdf-dev libssl-dev perl libx11-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-21 12:21:23 UTC
RemoteUrl: https://github.com/bioc/DEP
RemoteRef: HEAD
RemoteSha: c83f65987ca9787619c998ef654c07a110e2ec1a
NeedsCompilation: no
Packaged: 2026-10-02 23:11:51 UTC; root
Author: Jelmer Dijkstra [aut, cre],
  Arne Smits [aut],
  Wolfgang Huber [aut]
Maintainer: Jelmer Dijkstra <protechrobioMV@gmail.com>