joda

JODA algorithm for quantifying gene deregulation using knowledge

Bioconductor version: Development (3.0)

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 <szczurek at molgen.mpg.de>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("joda")

Documentation

PDF R Script Introduction to joda
PDF   Reference Manual

Details

biocViews GraphAndNetwork, Microarray, NetworkInference, Pathways, Software, StatisticalMethod
Version 1.13.0
In Bioconductor since BioC 2.8 (R-2.13)
License GPL (>= 2)
Depends R (>= 2.0), bgmm, RBGL
Imports
Suggests
System Requirements
URL http://www.bioconductor.org
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source joda_1.13.0.tar.gz
Windows Binary joda_1.13.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) joda_1.13.0.tgz
Mac OS X 10.9 (Mavericks)
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