To cite the protr package in your publication:

Xiao N, Cao D, Zhu M, Xu Q (2015). “protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences.” Bioinformatics, 31(11), 1857–1859. doi:10.1093/bioinformatics/btv042.

Corresponding BibTeX entry:

  @Article{,
    title = {protr/ProtrWeb: R package and web server for generating
      various numerical representation schemes of protein sequences},
    journal = {Bioinformatics},
    year = {2015},
    author = {Nan Xiao and Dong-Sheng Cao and Min-Feng Zhu and
      Qing-Song Xu},
    volume = {31},
    number = {11},
    pages = {1857--1859},
    doi = {10.1093/bioinformatics/btv042},
  }