# Gene regulatory network inference from single cell epigenomic data

## Documentation for package ‘epiregulon’ version 2.2.0

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

## Help Pages

addLogFC | Add log fold changes of gene expression to regulons
addMotifScore | Add Motif Scores
addTFMotifInfo | Add TF binding motif occupancy information to the peak2gene object
addWeights | Calculate weights for the regulons by computing co-association between TF and target gene expression
aggregateAcrossCellsFast | Aggregate cells in SingleCellExperiment
calculateActivity | Calculate the per cell activity of master regulators based on a regulon
calculateP2G | Establish peak to gene links based on correlations between ATAC-seq peaks and RNA-seq genes
getRegulon | Combine the TF binding info and peak to gene correlations to generate regulons
getTFMotifInfo | Retrieve TF binding sites or motif positions
optimizeMetacellNumber | Determine the optimal number of metacells to be used by 'calculateP2G' function
pruneRegulon | Prune regulons for true transcription factor - regulatory elements - target genes relationships