RT Journal Article
SR Electronic
T1 ChromVAR: Inferring transcription factor variation from single-cell epigenomic data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 110346
DO 10.1101/110346
A1 Alicia N. Schep
A1 Beijing Wu
A1 Jason D. Buenrostro
A1 William J. Greenleaf
YR 2017
UL http://biorxiv.org/content/early/2017/02/21/110346.abstract
AB 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.