To cite package ‘graphite’ in publications use:

  Sales G, Calura E, Cavalieri D, Romualdi C (2012). “graphite - a
  Bioconductor package to convert pathway topology to gene network.”
  _BMC Bioinformatics_.
  <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-20>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{graphite} - a Bioconductor package to convert pathway topology to gene network},
    author = {Gabriele Sales and Enrica Calura and Duccio Cavalieri and Chiara Romualdi},
    journal = {BMC Bioinformatics},
    year = {2012},
    url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-20},
  }

  Sales G, Calura E, Romualdi C (2018). “metaGraphite - a new layer of
  pathway annotation to get metabolite networks.” _Bioinformatics_.
  <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty719/5090451>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{metaGraphite} - a new layer of pathway annotation to get metabolite networks},
    author = {Gabriele Sales and Enrica Calura and Chiara Romualdi},
    journal = {Bioinformatics},
    year = {2018},
    url = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty719/5090451},
  }