AUTHORS

Cufflinks authors
Primary contact <cole@cs.umd.edu>

Cole Trapnell designed and wrote Cufflinks and Cuffdiff, with substantial technical input 
from Geo Pertea, Brian Williams, Ali Mortazavi, Jeltje van Baren, Steven Salzberg, Barbara Wold, 
and Lior Pachter. Geo Pertea wrote Cuffcompare.  Adam Roberts made substantial improvements to
the abundance estimation model used by Cufflinks and Cuffdiff.

"Tuxedo" Websites:
 Cufflinks:			 http://cufflinks.cbcb.umd.edu
 TopHat:			 http://tophat.cbcb.umd.edu
 Bowtie:             http://bowtie-bio.sf.net

As of version 1.0, Cufflinks depends on and includes LOCFIT, a regression package originally written 
by Catherine Loader and Jiayang Sun. Some modifications were made to LOCFIT.  Modified source
for LOCFIT lives in src/locfit.