To cite package ‘BaalChIP’ in publications use:

  de Santiago I, Liu W, Ke Y, Martin O, Chilamakuri C, A. J. Ponder B,
  B. Meyer K, Markowetz F (2017). “BaalChIP: Bayesian analysis of
  allele-specific transcription factor binding in cancer genomes.”
  _Genome Biology_, *18*(1), 39.
  <http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1165-7>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{BaalChIP}: Bayesian analysis of allele-specific transcription factor binding in cancer genomes},
    author = {Ines {de Santiago} and Wei Liu and Yuan Ke and O'Reilly Martin and Chandra Chilamakuri and Bruce {A. J. Ponder} and Kerstin {B. Meyer} and Florian Markowetz},
    year = {2017},
    journal = {Genome Biology},
    year = {2017},
    volume = {18},
    number = {1},
    pages = {39},
    url = {http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1165-7},
  }