JODA algorithm for quantifying gene deregulation using knowledge
Description
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).