DEqMS

DOI: 10.18129/B9.bioc.DEqMS    

a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

Bioconductor version: Release (3.8)

DEqMS is developped on top of Limma. However, Limma assumes same prior variance for all genes. In proteomics, the accuracy of protein abundance estimates varies by the number of peptides/PSMs quantified in both label-free and labelled data. Proteins quantification by multiple peptides or PSMs are more accurate. DEqMS package is able to estimate different prior variances for proteins quantified by different number of PSMs/peptides, therefore acchieving better accuracy. The package can be applied to analyze both label-free and labelled proteomics data.

Author: Yafeng Zhu

Maintainer: Yafeng Zhu <yafeng.zhu at ki.se>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DEqMS", version = "3.8")

Documentation

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

browseVignettes("DEqMS")

 

HTML R Script DEqMS R Markdown vignettes
PDF   Reference Manual
Text   NEWS

Details

biocViews Bayesian, DifferentialExpression, MassSpectrometry, MultipleComparison, Normalization, Preprocessing, Proteomics, Software
Version 1.0.0
License LGPL
Depends R (>= 3.5), graphics, stats, ggplot2, limma(>= 3.34)
Imports
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, plyr, matrixStats, reshape2, farms, RColorBrewer, utils, ggrepel, pheatmap, ExperimentHub
SystemRequirements
Enhances
URL
BugReports https://github.com/yafeng/DEqMS/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package DEqMS_1.0.0.tar.gz
Windows Binary DEqMS_1.0.0.zip
Mac OS X 10.11 (El Capitan) DEqMS_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DEqMS
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DEqMS
Package Short Url http://bioconductor.org/packages/DEqMS/
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: