# Mixture Nested Effects Models

## Documentation for package ‘mnem’ version 1.27.0

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

## Help Pages

app | Processed scRNAseq from pooled CRISPR screens
bootstrap | Bootstrap.
clustNEM | Cluster NEM.
createApp | Creating app data.
fitacc | Simulation accuracy.
fuzzyindex | Calculate fuzzy ground truth.
getAffinity | Calculate responsibilities.
getIC | Calculate negative penalized log likelihood.
hamSim | Accuracy for two phis.
mnem | Mixture NEMs - main function.
mnemh | Hierarchical mixture.
mnemk | Learn the number of components K and optimize the mixture.
moreboxplot | Boxplot with scatter and density options
nem | Implementation of the original NEM
plot.bootmnem | Plot bootstrap mnem result.
plot.mnem | Plot mnem result.
plot.mnem_mcmc | Plot mnem_mcmc result.
plot.mnem_sim | Plot simulated mixture.
plotConvergence | Plot convergence of EM
plotConvergence.mnem | Plot convergence of EM
plotDnf | Plot disjunctive normal form.
scoreAdj | Network score
simData | Simulate data.
transitive.closure | Transitive closure of a directed acyclic graph (dag)
transitive.reduction | Transitive reduction