Please cite deepTools as follows:
Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A. Grüning, and Thomas Manke. deepTools: a flexible platform for exploring deep-sequencing data. Nucl. Acids Res., 2014 doi:10.1093/nar/gku365

This tool suite is developed by the Bioinformatics Facility at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.