JODA algorithm for quantifying gene deregulation using knowledge

Documentation for package ‘joda’ version 1.30.0

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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.