To cite the 'MatrixEQTL' package in publications use:

Shabalin, Andrey A. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 28, no. 10 (2012): 1353-1358.

Corresponding BibTeX entry:

  @Article{,
    title = {Matrix {eQTL}: ultra fast {eQTL} analysis via large matrix
      operations},
    author = {A.A. Shabalin},
    address = {University of North Carolina at Chapel Hill},
    year = {2012},
    url =
      {http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/},
    publisher = {Oxford Univ Press},
    journal = {Bioinformatics},
    volume = {28},
    number = {10},
    pages = {1353--1358},
  }