gprege
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see gprege.
Gaussian Process Ranking and Estimation of Gene Expression time-series
Bioconductor version: 3.9
The gprege package implements the methodology described in Kalaitzis & Lawrence (2011) "A simple approach to ranking differentially expressed gene expression time-courses through Gaussian process regression". The software fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP kernel is initialised wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimised via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via ROC curves is performed against BATS (Angelini et.al, 2007). A detailed discussion of the ranking approach and dataset used can be found in the paper (http://www.biomedcentral.com/1471-2105/12/180).
Author: Alfredo Kalaitzis <alkalait at gmail.com>
Maintainer: Alfredo Kalaitzis <alkalait at gmail.com>
citation("gprege")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("gprege")
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("gprege")| gprege Quick Guide | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bioinformatics, DifferentialExpression, Microarray, Preprocessing, Software, TimeCourse |
| Version | 1.28.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (12 years) |
| License | AGPL-3 |
| Depends | R (>= 2.10), gptk |
| Imports | |
| System Requirements | |
| URL | |
| Bug Reports | alkalait@gmail.com |
See More
| Suggests | spam |
| Linking To | |
| Enhances | |
| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gprege_1.28.0.tar.gz |
| Windows Binary | gprege_1.28.0.zip |
| Mac OS X 10.11 (El Capitan) | gprege_1.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gprege |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gprege |
| Bioc Package Browser | https://code.bioconductor.org/browse/gprege/ |
| Package Short Url | https://bioconductor.org/packages/gprege/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |