Bioconductor version: Release (3.14)
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 (from within R,
enter citation("gprege")
):
To install this package, start R (version "4.1") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("gprege")
R Script | gprege Quick Guide | |
Reference Manual | ||
Text | NEWS |
biocViews | Bioinformatics, DifferentialExpression, Microarray, Preprocessing, Software, TimeCourse |
Version | 1.38.0 |
In Bioconductor since | BioC 2.10 (R-2.15) (10 years) |
License | AGPL-3 |
Depends | R (>= 2.10), gptk |
Imports | |
LinkingTo | |
Suggests | spam |
SystemRequirements | |
Enhances | |
URL | |
BugReports | alkalait@gmail.com |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | gprege_1.38.0.tar.gz |
Windows Binary | gprege_1.38.0.zip |
macOS 10.13 (High Sierra) | gprege_1.38.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/gprege |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gprege |
Package Short Url | https://bioconductor.org/packages/gprege/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.14 | Source Archive |
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