addConnections_peak_gene	addConnections_peak_gene
addConnections_TF_peak	addConnections_TF_peak
addData	addData
addData_TFActivity	addData_TFActivity
addSNPData	addSNPData
addTFBS	addTFBS
add_featureVariation	add_featureVariation
add_TF_gene_correlation	add_TF_gene_correlation
AR_classification_wrapper	AR_classification_wrapper
build_eGRN_graph	build_eGRN_graph
calculateCommunitiesEnrichment	calculateCommunitiesEnrichment
calculateCommunitiesStats	calculateCommunitiesStats
calculateGeneralEnrichment	calculateGeneralEnrichment
calculateTFEnrichment	calculateTFEnrichment
changeOutputDirectory	changeOutputDirectory
deleteIntermediateData	deleteIntermediateData
filterConnectionsForPlotting	filterConnectionsForPlotting
filterData	filterData
filterGRNAndConnectGenes	filterGRNAndConnectGenes
generateStatsSummary	generateStatsSummary
genes	nGenes
getCounts	getCounts
getGRNConnections	getGRNConnections
getGRNSummary	getGRNSummary
getParameters	getParameters
getTopNodes	getTopNodes
GRaNIE	GRaNIE
GRN-class	GRN-class
importTFData	importTFData
initializeGRN	initializeGRN
loadExampleObject	loadExampleObject
nGenes	nGenes
nPeaks	nPeaks
nTFs	nTFs
overlapPeaksAndTFBS	overlapPeaksAndTFBS
peaks	nPeaks
performAllNetworkAnalyses	performAllNetworkAnalyses
plotCommunitiesEnrichment	plotCommunitiesEnrichment
plotCommunitiesStats	plotCommunitiesStats
plotCorrelations	plotCorrelations
plotDiagnosticPlots_peakGene	plotDiagnosticPlots_peakGene
plotDiagnosticPlots_TFPeaks	plotDiagnosticPlots_TFPeaks
plotDiagnosticPlots_TFPeaks_GC	plotDiagnosticPlots_TFPeaks_GC
plotGeneralEnrichment	plotGeneralEnrichment
plotGeneralGraphStats	plotGeneralGraphStats
plotPCA_all	plotPCA_all
plotTFEnrichment	plotTFEnrichment
plot_stats_connectionSummary	plot_stats_connectionSummary
TFs	nTFs
visualizeGRN	visualizeGRN
