# JODA algorithm for quantifying gene deregulation using knowledge

## Documentation for package ‘joda’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

beliefs.damage | Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
beliefs.healthy | Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
data.damage | Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
data.healthy | Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
deregulation.p.values | Calculating deregulation p-values using resampling method.
deregulation.scores | Calculating deregulation scores.
differential.probs | Calculating probabilities of differential expression in perturbation experiments
model.damage | Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
model.healthy | Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
regulation.scores | Calculating regulation scores.