DEP

DOI: 10.18129/B9.bioc.DEP  

Differential Enrichment analysis of Proteomics data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	DataRepresentation, DifferentialExpression, ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 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
LinkingTo
Suggests	testthat, enrichR, knitr, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	proDA, RforProteomics
Links To Me
Build Report

Package Archives

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

Source Package	DEP_1.20.0.tar.gz
Windows Binary	DEP_1.20.0.zip
macOS Binary (x86_64)	DEP_1.20.0.tgz
macOS Binary (arm64)	DEP_1.20.0.tgz
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