If you have ChIA-PET data, and are interested in finding significant interactions based on the NCHG model. I have developed, and am actively maintaining a software suit called ChiaSig.

Software accompanying the publication Paulsen et al. (2014) A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions. can be found here.

Interactions reported as significant in the paper:
K562Pol2.NCHG.sig.bed
Mcf7Pol2.NCHG.sig.bed
K562Pol2.NCHG.sig.bedpe
Mcf7Pol2.NCHG.sig.bedpe


Jonas Paulsen Tue Apr 7 15:13:12 2015