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msmsTests

LC-MS/MS Differential Expression Tests


Bioconductor version: Release (3.18)

Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.

Author: Josep Gregori, Alex Sanchez, and Josep Villanueva

Maintainer: Josep Gregori i Font <josep.gregori at gmail.com>

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

Installation

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


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

BiocManager::install("msmsTests")

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("msmsTests")
msmsTests: controlling batch effects by blocking PDF R Script
msmsTests: post test filters to improve reproducibility PDF R Script
Reference Manual PDF

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 1.40.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-2
Depends R (>= 3.0.1), MSnbase, msmsEDA
Imports edgeR, qvalue
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Package Archives

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

Source Package msmsTests_1.40.0.tar.gz
Windows Binary msmsTests_1.40.0.zip
macOS Binary (x86_64) msmsTests_1.40.0.tgz
macOS Binary (arm64) msmsTests_1.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/msmsTests
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/msmsTests
Bioc Package Browser https://code.bioconductor.org/browse/msmsTests/
Package Short Url https://bioconductor.org/packages/msmsTests/
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