To cite package ‘chromVAR’ in publications use:

  Schep, A.N., Wu, B., Buenrostro, J.D., Greenleaf W.J. chromVAR:
  inferring transcription-factor-associated accessibility from
  single-cell epigenomic data Nature Methods (2017)

A BibTeX entry for LaTeX users is

  @Article{,
    title = {chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data},
    author = {Alicia N Schep and Beijing Wu and Jason D Buenrostro and William J Greenleaf},
    year = {2017},
    journal = {Nature Methods},
    doi = {10.1038/nmeth.4401},
  }