To install this package, start R and enter:

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

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

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>

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

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

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