DEP

This is the development version of DEP; for the stable release version, see DEP.

Differential Enrichment analysis of Proteomics data

Bioconductor version: Development (3.21)

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 <smits.arne at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DEP")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DEP")

DEP: Introduction	HTML	R Script
DEP: Missing value handling	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, DifferentialExpression, ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.29.0
In Bioconductor since	BioC 3.6 (R-3.4) (7 years)
License	Artistic-2.0
Depends	R (>= 3.5)
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
System Requirements
URL

Suggests	testthat, enrichR, knitr, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	proDA, RforProteomics
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	DEP_1.29.0.tar.gz
Windows Binary (x86_64)	DEP_1.29.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/DEP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DEP
Bioc Package Browser	https://code.bioconductor.org/browse/DEP/
Package Short Url	https://bioconductor.org/packages/DEP/
Package Downloads Report	Download Stats