To cite package ‘DESeq2’ in publications use:

  Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change
  and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550
  (2014)

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
    author = {Michael I. Love and Wolfgang Huber and Simon Anders},
    year = {2014},
    journal = {Genome Biology},
    doi = {10.1186/s13059-014-0550-8},
    volume = {15},
    issue = {12},
    pages = {550},
  }