DOI: 10.18129/B9.bioc.joda    

This is the development version of joda; for the stable release version, see joda.

JODA algorithm for quantifying gene deregulation using knowledge

Bioconductor version: Development (3.9)

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>

Citation (from within R, enter citation("joda")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("joda", version = "3.9")

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:



PDF R Script Introduction to joda
PDF   Reference Manual


biocViews GraphAndNetwork, Microarray, NetworkInference, Pathways, Software, StatisticalMethod
Version 1.31.0
In Bioconductor since BioC 2.8 (R-2.13) (7.5 years)
License GPL (>= 2)
Depends R (>= 2.0), bgmm, RBGL
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