To cite paxtoolsr:

  Luna, A et al. PaxtoolsR: Pathway Analysis in R Using Pathway
  Commons. 2015 Dec. http://www.ncbi.nlm.nih.gov/pubmed/26685306

A BibTeX entry for LaTeX users is

  @Article{,
    author = {{Luna} and {A.} and {Babur} and {O.} and {Aksoy} and B. A. and {Demir} and {E.} and {Sander} and {C.}},
    title = {{{P}axtools{R}: {P}athway {A}nalysis in {R} {U}sing {P}athway {C}ommons}},
    journal = {Bioinformatics},
    year = {2015},
    month = {Dec},
  }

This free open-source software implements academic research by the
authors. Its development took a large amount of extra time and effort.
If you use it, please support the project by citing the listed journal
articles.