# Gene regulatory network inference from single cell epigenomic data

## Documentation for package ‘epiregulon’ version 1.0.1

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

## 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
aggregateAcrossCells | Aggregate expression across cells
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
pruneRegulon | Prune regulons for true transcription factor - regulatory elements - target genes relationships