chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

Nat Methods. 2017 Oct;14(10):975-978. doi: 10.1038/nmeth.4401. Epub 2017 Aug 21.


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

MeSH terms

  • Algorithms
  • Animals
  • Cell Line
  • Epigenomics / methods*
  • Gene Expression Regulation
  • Sequence Analysis, DNA / methods*
  • Software*
  • Transcription Factors / metabolism*


  • Transcription Factors