DEP

DOI: 10.18129/B9.bioc.DEP    

Differential Enrichment analysis of Proteomics data

Bioconductor version: Release (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 embl.de>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DEP")

Documentation

HTML	R Script	DEP package
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, DifferentialExpression, MassSpectrometry, Proteomics, Software
Version	1.0.1
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, imputeLCMD
LinkingTo
Suggests	testthat, enrichR, knitr, BiocStyle
SystemRequirements
Enhances
URL
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_1.0.1.tar.gz
Windows Binary	DEP_1.0.1.zip
Mac OS X 10.11 (El Capitan)	DEP_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DEP
Package Short Url	http://bioconductor.org/packages/DEP/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive