joda

JODA algorithm for quantifying gene deregulation using knowledge

Bioconductor version: Development (2.8)

Package 'joda' implements three steps of an algorithm called JODA. The algorithm computes gene deregulation scores. For each gene, its deregulation score reflects how strongly an effect of a certain regulator's perturbation on this gene differs between two different cell populations. The algorithm utilizes regulator knockdown expression data as well as knowledge about signaling pathways in which the regulators are involved (formalized in a simple matrix model).

Author: Ewa Szczurek

Maintainer: Ewa Szczurek

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("joda")    

Documentation

PDF

R Script

Introduction to joda

Reference Manual

Details

biocViews	Microarray, Bioinformatics, Pathways, GraphsAnNetworks, Statistics
Depends	R, bgmm, RBGL
Imports
Suggests
System Requirements
License	GPL (>= 2)
URL	http://www.bioconductor.org
Depends On Me
Imports Me
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Version	0.99.0

Package Downloads

Package Source	joda_0.99.0.tar.gz
Windows Binary	joda_0.99.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	joda_0.99.0.tgz
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