chromVAR: Inferring transcription factor variation from single-cell epigenomic data

Single cell ATAC-seq (scATAC) yields sparse data that makes application of conventional computational approaches for data analysis challenging or impossible. We developed chromVAR, an R package for analyzing sparse chromatin accessibility data by estimating the gain or loss of accessibility within sets of peaks sharing the same motif or annotation while controlling for known technical biases. chromVAR enables accurate clustering of scATAC-seq profiles and enables characterization of known, or the de novo identification of novel, sequence motifs associated with variation in chromatin accessibility across single cells or other sparse epigenomic data sets.