addConnections_peak_gene	addConnections_peak_gene
addConnections_TF_peak	addConnections_TF_peak
addData	addData
addData_TFActivity	addData_TFActivity
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
filterData	filterData
filterGRNAndConnectGenes	filterGRNAndConnectGenes
generateStatsSummary	generateStatsSummary
genes	genes-methods
genes	nGenes
getCounts	getCounts
getGRNConnections	getGRNConnections
getGRNSummary	getGRNSummary
getParameters	getParameters
getTopNodes	getTopNodes
GRaNIE	GRaNIE
GRN-class	GRN-class
importTFData	importTFData
initializeGRN	initializeGRN
installSuggestedPackages	installSuggestedPackages
loadExampleObject	loadExampleObject
nGenes	genes-methods
nGenes	nGenes
nPeaks	nPeaks
nPeaks	peaks-methods
nTFs	nTFs
overlapPeaksAndTFBS	overlapPeaksAndTFBS
peaks	nPeaks
peaks	peaks-methods
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
