DEqMS

DOI: 10.18129/B9.bioc.DEqMS  

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

Bioconductor version: Release (3.16)

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 outlook.com>

Installation

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

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

BiocManager::install("DEqMS")

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("DEqMS")

 

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

Details

biocViews	Bayesian, DifferentialExpression, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Preprocessing, Proteomics, Software
Version	1.16.0
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 years)
License	LGPL
Depends	R (>= 3.5), graphics, stats, ggplot2, matrixStats, limma(>= 3.34)
Imports
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, markdown, plyr, reshape2, farms, utils, ggrepel, ExperimentHub, LSD
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_1.16.0.tar.gz
Windows Binary	DEqMS_1.16.0.zip
macOS Binary (x86_64)	DEqMS_1.16.0.tgz
macOS Binary (arm64)	DEqMS_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DEqMS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DEqMS
Bioc Package Browser	https://code.bioconductor.org/browse/DEqMS/
Package Short Url	https://bioconductor.org/packages/DEqMS/
Package Downloads Report	Download Stats