# epiNEM

## Documentation for package ‘epiNEM’ version 1.34.0

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

## Help Pages

AddLogicGates | Add logic.
CreateExtendedAdjacency | Create an extended adjacency matrix
CreateRandomGraph | Create a random graph
CreateTopology | Create Topology.
epiAnno | Gate visualisation.
epiNEM | Epistatic NEMs - main function.
epiScreen | Analyse large double knock-out screen.
ExtendTopology | Extending topology of normal "nem"
GenerateData | Generate data from extended model.
HeatmapOP | Heatmap.
Mll | Evaluation of graphs
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
SimEpiNEM | Compare algorithms.
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"