Gene regulatory network inference from single cell epigenomic data

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Documentation for package ‘epiregulon’ version 1.2.0

• 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