buildGraph              Creating graphs and related operations
calculateJaccardSimilarity
                        Calculate Jaccard Similarity between regulons
                        of all transcription factors
enrichPlot              Plot results of regulonEnrich
findDifferentialActivity
                        Test for differential TF activity between pairs
                        of single cell clusters/groups
findPartners            Find interaction partners of a transcription
                        factor of interest
getSigGenes             Compile and summarize the output from
                        findDifferentialActivity function
permuteGraph            Calculate similarity score from permuted graphs
                        to estimate background similarity
plotActivityDim         Plot cell-level reduced dimension results
                        stored in a SingleCellExperiment object,
                        colored by activities for a list of TFs
plotActivityViolin      Generate violin plots of inferred activities
                        for a list of TFs grouped by cluster/group
                        labels
plotBubble              Generate bubble plots of relative activities
                        across cluster/group labels for a list of TFs
plotDiffNetwork         Plot graph according to grouping factor
plotEpiregulonNetwork   Plot a graph build based on 'getRegulon' output
plotGseaNetwork         Plot networks graph of significant genesets
                        from regulonEnrich results
plotHeatmapActivity     Plot transcription factor activity
plotHeatmapRegulon      Plot targets genes of transcription factors in
                        regulons
regulon                 regulon created using 'epiregulon' package from
                        reprogram-seq data
regulonEnrich           Perform geneset enrichment of user-defined
                        regulons
