msmsTests

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see msmsTests.

LC-MS/MS Differential Expression Tests

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	1.32.0
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
System Requirements
URL

Suggests
Linking To
Enhances
Depends On Me
Imports Me	MSnID
Suggests Me	RforProteomics
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	msmsTests_1.32.0.tar.gz
Windows Binary	msmsTests_1.32.0.zip
macOS 10.13 (High Sierra)	msmsTests_1.32.0.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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive