Package: DEP
Title: Differential Enrichment analysis of Proteomics data
Version: 1.31.0
Authors@R: c(
    person("Arne", "Smits", email = "smits.arne@gmail.com", role = c("cre", "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 (>= 3.5)
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
RoxygenNote: 6.1.1
Suggests: testthat, enrichR, knitr, BiocStyle
biocViews: ImmunoOncology, Proteomics, MassSpectrometry,
        DifferentialExpression, DataRepresentation
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/DEP
git_branch: devel
git_last_commit: 67db94e
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-04 22:34:48 UTC; biocbuild
Author: Arne Smits [cre, aut],
  Wolfgang Huber [aut]
Maintainer: Arne Smits <smits.arne@gmail.com>
Built: R 4.5.0; ; 2025-06-05 12:50:42 UTC; windows
