DEP

DOI: 10.18129/B9.bioc.DEP    

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

Differential Enrichment analysis of Proteomics data

Bioconductor version: Development (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DEP", version = "devel")

Documentation

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

browseVignettes("DEP")

 

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

Details

biocViews DataRepresentation, DifferentialExpression, MassSpectrometry, Proteomics, Software
Version 1.3.3
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
LinkingTo
Suggests testthat, enrichR, knitr, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me RforProteomics
Links To Me
Build Report  

Package Archives

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

Source Package DEP_1.3.3.tar.gz
Windows Binary DEP_1.3.3.zip
Mac OS X 10.11 (El Capitan) DEP_1.3.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/DEP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DEP
Package Short Url http://bioconductor.org/packages/DEP/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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