DEqMS
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
Bioconductor version: Release (3.20)
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("DEqMS")):
Installation
To install this package, start R (version "4.4") 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")| DEqMS R Markdown vignettes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, DifferentialExpression, ExperimentHubSoftware, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Preprocessing, Proteomics, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (6 years) |
| License | LGPL |
| Depends | R (>= 3.5), graphics, stats, ggplot2, matrixStats, limma(>= 3.34) |
| Imports | |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/yafeng/DEqMS/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, markdown, plyr, reshape2, utils, ggrepel, ExperimentHub, LSD |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | PRONE |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DEqMS_1.24.0.tar.gz |
| Windows Binary (x86_64) | DEqMS_1.24.0.zip (64-bit only) |
| macOS Binary (x86_64) | DEqMS_1.24.0.tgz |
| macOS Binary (arm64) | DEqMS_1.23.4.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 |