joda: JODA algorithm for quantifying gene deregulation using knowledge

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).

Package details

AuthorEwa Szczurek
Bioconductor views GraphAndNetwork Microarray NetworkInference Pathways StatisticalMethod
MaintainerEwa Szczurek <>
LicenseGPL (>= 2)
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


Try the joda package in your browser

Any scripts or data that you put into this service are public.

joda documentation built on April 28, 2020, 8:35 p.m.