To cite package ‘CAGEr’ in publications use:

  Haberle V, Forrest ARR, Hayashizaki Y, Carninci P, Lenhard B (2015)
  CAGEr: precise TSS data retrieval and high-resolution promoterome
  mining for integrative analyses. Nucleic Acids Res 43(8):e51.
  doi:10.1093/nar/gkv054

A BibTeX entry for LaTeX users is

  @Article{,
    title = {CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses},
    author = {Vanja Haberle and Alistair R R Forrest and Yoshihide Hayashizaki and Piero Carninci and Boris Lenhard},
    year = {2015},
    journal = {Nucleic Acids Research},
    volume = {43},
    issue = {8},
    pages = {e51},
    doi = {10.1093/nar/gkv054},
    url = {http://nar.oxfordjournals.org/content/43/8/e51},
  }