To cite package ‘apeglm’ in publications use:

  Zhu, A., Ibrahim, J.G., Love, M.I. Heavy-tailed prior distributions
  for sequence count data: removing the noise and preserving large
  differences Bioinformatics (2018)

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences},
    author = {Anqi Zhu and Joseph G. Ibrahim and Michael I. Love},
    year = {2018},
    journal = {Bioinformatics},
    doi = {10.1093/bioinformatics/bty895},
  }