AddLogicGates           Add logic.
CreateExtendedAdjacency
                        Create an extended adjacency matrix
CreateRandomGraph       Create a random graph
CreateTopology          Create Topology.
ExtendTopology          Extending topology of normal "nem"
GenerateData            Generate data from extended model.
HeatmapOP               Heatmap.
Mll                     Evaluation of graphs
SimEpiNEM               Compare algorithms.
epiAnno                 Gate visualisation.
epiNEM                  Epistatic NEMs - main function.
epiScreen               Analyse large double knock-out screen.
perm.rank.test          AUC permutation test
plot.epiNEM             Plot pathway.
plot.epiScreen          Plot screen.
plot.epiSim             Plot simulations.
rank.enrichment         Rank enrichment
sameith_GO              graph-based GO similarity scores, string GO
                        annotations for Sameith et al., 2015 data
sameith_string          sig. of string interaction scores for Sameith
                        et al., 2015 data
samscreen               Example data: epiNEM results for the Sameith et
                        al., 2015 knock-out screen
sim                     Example data: simulation results
wageningen_GO           graph-based GO similarity scores, string GO
                        annotations for van Wageningen et al., 2015
                        data
wageningen_string       sig. of string interaction scores for van
                        Wageningen et al., 2010 data
wagscreen               Example data: epiNEM results for the Wageningen
                        et al., 2010 knock-out screen
                        "http://www.holstegelab.nl/publications/GSTF_geneticinteractions/
                        downloads/del_mutants_limma.txt"
