Gene regulatory network inference from single cell epigenomic data


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Documentation for package ‘epiregulon’ version 1.3.5

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