To install this package, start R and enter:

## try http:// if https:// URLs are not supported

In most cases, you don't need to download the package archive at all.


DOI: 10.18129/B9.bioc.DEP    

This is the development version of DEP; to use it, please install the devel version of Bioconductor.

Differential Enrichment analysis of Proteomics data

Bioconductor version: Development (3.6)

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.

Author: Arne Smits [cre, aut], Wolfgang Huber [aut]

Maintainer: Arne Smits <arne.smits at>

Citation (from within R, enter citation("DEP")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


HTML R Script DEP package
PDF   Reference Manual
Text   NEWS


biocViews DataRepresentation, DifferentialExpression, MassSpectrometry, Proteomics, Software
Version 0.99.4
License Artistic-2.0
Depends R (>= 3.4)
Imports ggplot2, dplyr, purrr, readr, tibble, tidyr, broom, Biobase, SummarizedExperiment, MSnbase, limma, vsn, fdrtool, ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny, shinydashboard, DT, rmarkdown, assertthat, gridExtra, grid, stats
Suggests testthat, enrichR, knitr, BiocStyle
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DEP_0.99.4.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) DEP_0.99.4.tgz
Source Repository git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: