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 (from within R, enter 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 PDF R Script
Reference Manual PDF
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
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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