To cite the R package 'HTSFilter' in publications use:

  A. Rau, M. Gallopin, G. Celeux, F. Jaffrezic (2013). Data-based
  filtering for replicated high-throughput transcriptome sequencing
  experiments. Bioinformatics 29(17): 2146-2152. doi:
  10.1093/bioinformatics/btt350.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Data-based filtering for replicated high-throughput transcriptome sequencing experiments},
    year = {2013},
    journal = {Bioinformatics},
    volume = {29},
    number = {17},
    pages = {2146-2152},
    author = {Andrea Rau and Melina Gallopin and Gilles Celeux and Florence Jaffrezic},
  }