# Companion package to epiregulon with additional plotting, differential and graph functions

## Documentation for package ‘epiregulon.extra’ version 1.8.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

addCentrality | Creating graphs and related operations
buildDiffGraph | Creating graphs and related operations
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
normalizeCentrality | Creating graphs and related operations
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
rankTfs | Creating graphs and related operations
regulon | regulon created using 'epiregulon' package from reprogram-seq data
regulonEnrich | Perform geneset enrichment of user-defined regulons