msmsTests
LC-MS/MS Differential Expression Tests
Bioconductor version: Release (3.20)
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("msmsTests")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| msmsTests: post test filters to improve reproducibility | R Script | |
| Reference Manual |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Proteomics, Software |
| Version | 1.44.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (11 years) |
| License | GPL-2 |
| Depends | R (>= 3.0.1), MSnbase, msmsEDA |
| Imports | edgeR, qvalue |
| System Requirements | |
| URL |
See More
| Suggests | xtable |
| 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_1.44.0.tar.gz |
| Windows Binary (x86_64) | msmsTests_1.44.0.zip |
| macOS Binary (x86_64) | msmsTests_1.44.0.tgz |
| macOS Binary (arm64) | msmsTests_1.44.0.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 |