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.
add_featureVariation    Quantify and interpret multiple sources of
                        biological and technical variation for features
                        (TFs, peaks, and genes) in a 'GRN' object
build_eGRN_graph        Builds a graph out of a set of connections
calculateCommunitiesEnrichment
                        Run an enrichment analysis for the genes in
                        each community in the filtered 'GRN' object
calculateCommunitiesStats
                        Generate graph communities and their
                        summarizing statistics
calculateGeneralEnrichment
                        Run an enrichment analysis for the genes in the
                        whole network in the filtered 'GRN' object
calculateTFEnrichment   Run an enrichment analysis for the set of genes
                        connected to a particular TF or sets of TFs in
                        the filtered 'GRN' object
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 RNA-seq and/or peak data from a 'GRN'
                        object
filterGRNAndConnectGenes
                        Filter TF-peaks and peak-gene connections and
                        combine them to TF-peak-gene connections to
                        construct an eGRN.
generateStatsSummary    Generate a summary for the number of
                        connections for different filtering criteria
                        for a 'GRN' object.
getCounts               Get counts for the various data defined in a
                        'GRN' object
getGRNConnections       Extract connections or links from a 'GRN'
                        object as a data frame.
getGRNSummary           Summarize a 'GRN' object to a named list for
                        comparison with other 'GRN' objects.
getParameters           Retrieve parameters for previously used
                        function calls and general parameters for a
                        'GRN' object.
getTopNodes             Retrieve the top nodes (TFs or genes) with
                        respect to either degree or Eigenvector
                        centrality in the filtered 'GRN' object.
importTFData            Import externally derived TF Activity data.
                        EXPERIMENTAL.
initializeGRN           Create and initialize an empty 'GRN' object.
installSuggestedPackages
                        Automatically install all suggested packages
                        for the 'GRaNIE' package
loadExampleObject       Load example GRN dataset
nGenes                  Get the number of genes for a 'GRN' object.
nGenes                  Get the number of genes for a 'GRN' object.
nPeaks                  Get the number of peaks for a 'GRN' object.
nPeaks                  Get the number of peaks for a 'GRN' object.
nTFs                    Get the number of TFs 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. See the functions it
                        executes in the @seealso section below.
plotCommunitiesEnrichment
                        Plot community-based enrichment results for a
                        filtered 'GRN' object
plotCommunitiesStats    Plot general structure & connectivity
                        statistics for each community in a filtered
                        'GRN'
plotCorrelations        Plot scatter plots of the underlying count data
                        for either TF-peak, peak-gene or TF-gene pairs
                        for a 'GRN' object
plotDiagnosticPlots_TFPeaks
                        Plot diagnostic plots for TF-peak connections
                        for a 'GRN' object
plotDiagnosticPlots_TFPeaks_GC
                        Plot GC-specific 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' object
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 eGRN in a flexible manner.
