AR_classification_wrapper
                        Run the activator-repressor classification for
                        the TFs for a 'GRN' object
GRN-class               Create, represent, investigate, quantify and
                        visualize enhancer-mediated gene regulatory
                        networks (*eGRNs*)
GRaNIE                  *GRaNIE* (*G*ene *R*egul*a*tory *N*etwork
                        *I*nference including *E*nhancers):
                        Reconstruction and evaluation of data-driven,
                        cell type specific gene regulatory networks
                        including enhancers using chromatin
                        accessibility and RNAseq data (general package
                        information)
addConnections_TF_peak
                        Add TF-peak connections to a 'GRN' object
addConnections_peak_gene
                        Add peak-gene connections to a 'GRN' object
addData                 Add data to a 'GRN' object
addData_TFActivity      Add TF activity data to GRN object using a
                        simplified procedure for estimating it.
                        EXPERIMENTAL.
addTFBS                 Add TFBS to a 'GRN' object
add_TF_gene_correlation
                        Add TF-gene correlations to a 'GRN' object. The
                        information is currently stored in
                        'GRN@connections$TF_genes.filtered'. Note that
                        raw p-values are not adjusted.
build_eGRN_graph        Builds a graph out of a set of connections
calculateCommunitiesEnrichment
                        Enrichment analysis for the genes in each
                        community in the filtered 'GRN'
calculateCommunitiesStats
                        Generate graph communities and their
                        summarizing statistics
calculateGeneralEnrichment
                        Run an enrichment analysis for the genes in the
                        filtered 'GRN'
calculateTFEnrichment   Calculate TF-based GO enrichment
changeOutputDirectory   Change the output directory of a GRN object
deleteIntermediateData
                        Optional convenience function to delete
                        intermediate data from the function
                        'AR_classification_wrapper' and summary
                        statistics that may occupy a lot of space
filterData              Filter data from a 'GRN' object
filterGRNAndConnectGenes
                        Filter the GRN and integrate peak-gene
                        connections.
generateStatsSummary    Generate a summary PDF for the number of
                        connections for a 'GRN' object.
getCounts               Get counts for the various data defined in a
                        'GRN' object
getGRNConnections       Extract connections from a 'GRN' object
getParameters           Retrieve parameters for previously used
                        function calls and general parameters for a
                        'GRN' object.
getTopNodes             Retrieve top Nodes in the filtered 'GRN'
importTFData            Import externally derived TF Activity data.
                        EXPERIMENTAL.
initializeGRN           Initialize a 'GRN' object
loadExampleObject       Load example GRN dataset
nGenes                  Get the number of genes for a 'GRN' object.
nPeaks                  Get the number of peaks for a 'GRN' object.
overlapPeaksAndTFBS     Overlap peaks and TFBS for a 'GRN' object
performAllNetworkAnalyses
                        Perform all network-related statistical and
                        descriptive analyses, including community and
                        enrichment analyses.
plotCommunitiesEnrichment
                        Plot community-based enrichment results
plotCommunitiesStats    Plot general structure & connectivity
                        statistics for each community in a filtered
                        'GRN'
plotDiagnosticPlots_TFPeaks
                        Plot diagnostic plots for TF-peak connections
                        for a 'GRN' object
plotDiagnosticPlots_peakGene
                        Plot diagnostic plots for peak-gene connections
                        for a 'GRN' object
plotGeneralEnrichment   Plot the general enrichement results
plotGeneralGraphStats   Plot general structure and connectivity
                        statistics for a filtered 'GRN'
plotPCA_all             Produce a PCA plot of the data from a 'GRN'
                        object
plotTFEnrichment        Plot TF-based GO enrichment results
plot_stats_connectionSummary
                        Plot various network connectivity summaries for
                        a 'GRN' object
visualizeGRN            Visualize a filtered GRN.
