The code used to process and analyze single-cell Hi-C libraries in the paper: 

<a href="http://www.nature.com/nature/journal/v547/n7661/full/nature23001.html" target="_blank">Cell-cycle dynamics of chromosomal organization at single-cell resolution</a> by  Takashi Nagano, Yaniv Lubling, Csilla Várnai, Carmel Dudley, Wing Leung, Yael Baran, Netta Mendelson Cohen, Steven Wingett, Peter Fraser & Amos Tanay, Nature, 2017

is available in the public repository: <a href="https://bitbucket.org/tanaylab/schic2/overview" target="_blank">schic2</a>