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

S. Balzergue, G. Rigaill, V. Brunaud, E. Blondet, A. Rau, O. Rogier, J. Caius, C. Maugis-Rabusseau, L. Soubigou-Taconnat, S. Aubourg, C. Lurin, E. Delannoy, and M.-L. Martin-Magniette. (2014) HTSDiff: A Model-Based Clustering Alternative to Test-Based Methods in Differential Gene Expression Analyses by RNA-Seq Benchmarked on Real and Synthetic Datasets (submitted).

Corresponding BibTeX entry:

    title = {HTSDiff: a sensitive analysis of differential gene
      expression by RNA-seq (submitted)},
    year = {2014},
    journal = {(submitted)},
    author = {S. Balzergue and G. Rigaill and V. Brunaud and E. Blondet
      and A. Rau and O. Rogier and J. Caius and C. Maugis-Rabusseau and
      L. Soubigou-Taconnat and S. Aubourg and C. Lurin and E. Delannoy
      and M.-L. Martin-Magniette},