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
