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DEqMS

This is the development version of DEqMS; for the stable release version, see DEqMS.

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

Bioconductor version: Development (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Bayesian, DifferentialExpression, ExperimentHubSoftware, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Preprocessing, Proteomics, Software
Version 1.19.0
In Bioconductor since BioC 3.8 (R-3.5) (5 years)
License LGPL
Depends R (>= 3.5), graphics, stats, ggplot2, matrixStats, limma(>= 3.34)
Imports
Linking To
Suggests BiocStyle, knitr, rmarkdown, markdown, plyr, reshape2, farms, utils, ggrepel, ExperimentHub, LSD
System Requirements
Enhances
URL
Bug Reports https://github.com/yafeng/DEqMS/issues
See More
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_1.19.0.tar.gz
Windows Binary DEqMS_1.19.0.zip
macOS Binary (x86_64) DEqMS_1.19.0.tgz
macOS Binary (arm64) DEqMS_1.19.0.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