msmsTests
This is the released version of msmsTests; for the devel version, see msmsTests.
LC-MS/MS Differential Expression Tests
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.50.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 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_1.50.0.tar.gz |
| Windows Binary (x86_64) | msmsTests_1.50.0.zip |
| macOS Binary (big-sur-x86_64) | msmsTests_1.50.0.tgz |
| macOS Binary (sonoma-arm64) | msmsTests_1.50.0.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 |