DEP
This is the development version of DEP; to use it, please install the devel version of Bioconductor.
Differential Enrichment analysis of Proteomics data
DOI: 10.18129/B9.bioc.DEP
Bioconductor version: Development (3.24)
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: Jelmer Dijkstra [aut, cre], Arne Smits [aut], Wolfgang Huber [aut]
Maintainer: Jelmer Dijkstra <protechrobioMV at gmail.com>
citation("DEP")):Jelmer Dijkstra, Arne Smits, Wolfgang Huber. DEP: Differential Enrichment analysis of Proteomics data. doi:10.18129/B9.bioc.DEP, R package version 3.99.0, https://bioconductor.org/packages/DEP.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, DifferentialExpression, ImmunoOncology, MassSpectrometry, Proteomics, Software |
| Version | 3.99.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| 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 |
See More
| Suggests | testthat, enrichR, knitr, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DEP_3.99.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | DEP_3.99.0.tgz |
| macOS Binary (sonoma-arm64) | |
| 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 | https://bioconductor.org/packages/DEP/ |
| Package Downloads Report | Download Stats |