DiNuP is implemented by Python and freely avialable.
The latest version of DiNuP is DiNuP_1.3 

Noting: We suggest the users to use BED files with no more than 5-pile reads. 5-pile means 
there are at least 5 reads have exactly the same chromosome, position and strand.

We also applied DiNuP to several publicly datasets, we put the identified regions of
differential nucleosome here.

Kaplan et al. Nature 2009: DiNuP_Result_Kaplan.zip  

Shivaswamy et al. Plos Biology 2008: DiNuP_Result_Schones.zip  

Schones et al. Cell 2008: DiNuP_Result_Shivaswamy.zip  

2012-8-24
DiNuP 1.3:
Fix a serious of bugs. Thanks Alex!

2012-2-9
DiNuP 1.2:
Integrate fold change method into DiNuP (see README);

2011-12-30
DiNuP 1.1: 
Improve FDR calculating;

2011-10-4
DiNuP alpha: 
DiNuP alpha becomes publicly avilable!
 

If you have any questions, suggestions, bug reports, etc, feel free to contact
Kai Fu (kelvinfu dot tju at gmail dot com)