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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("msmsTests")
In most cases, you don't need to download the package archive at all.
msmsTests
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see msmsTests.
LC-MS/MS Differential Expression Tests
Bioconductor version: 3.3
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("msmsTests")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("msmsTests")
| R Script | msmsTests: controlling batch effects by blocking | |
| R Script | msmsTests: post test filters to improve reproducibility | |
| Reference Manual |
Details
| biocViews | MassSpectrometry, Proteomics, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (3 years) |
| License | GPL-2 |
| Depends | R (>= 3.0.1), MSnbase, msmsEDA |
| Imports | edgeR, qvalue |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | MSnID, RforProteomics |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | msmsTests_1.10.0.tar.gz |
| Windows Binary | msmsTests_1.10.0.zip |
| Mac OS X 10.9 (Mavericks) | msmsTests_1.10.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/msmsTests/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/msmsTests/ |
| Package Downloads Report | Download Stats |
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