# Training of logical models from indirect measurements of perturbation experiments

## Documentation for package ‘bnem’ version 1.0.0

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

## Help Pages

absorption | Absorption
absorptionII | Inverse absorption
addNoise | Add noise
bcr | B-Cell receptor signalling perturbations
bnem | Boolean Nested Effects Model main function
bnemBs | Bootstraped Network
computeFc | Compute differential effects
convertGraph | Convert normal form
dummyCNOlist | Create dummy CNOlist
epiNEM2Bg | Switch between epiNEM and B-NEM
findResiduals | Compute residuals
plot.bnem | plot bnem opbject
plot.bnemBs | Plot Bootstrap result
plot.bnemsim | plot simulation object
processDataBCR | BCR perturbation reproduction
randomDnf | sample normal form
reduceGraph | Reduce graph
scoreDnf | score a boolean network
simBoolGtn | Sample random network and simulate data
simulateStatesRecursive | Simulate states
transClose | transitive closure
transRed | transitive reduction
validateGraph | validate graph