Juicebox is visualization software for Hi-C data. In this distribution, we include both the visualization software itself and command line tools for creating and analyzing files that can be loaded into Juicebox.

If you use Juicebox in your research, please cite:

Neva C. Durand, James T. Robinson, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, and Erez Lieberman Aiden. "Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom." Cell Systems 3(1), 2016.

Please see the wiki for extensive documentation. We also have an active Google groups forum for questions and answers.

Juicebox was created by Jim Robinson, Neva C. Durand, and Erez Lieberman Aiden.

Ongoing development work is carried out by Neva C. Durand, Fanny Huang, Ido Machol, and Muhammad Saad Shamim.

Past contributors include Zulkifl Gire, Marie Hoeger, Nam Hee Kim, Vi Nguyen, and Jay Ryu.

The files included in this distribution are as follows:

• README
• build.xml and juicebox.properties (for jar compilation from source)
• src (directory containing source code)
• lib (directory containing libraries for compilation)
• data (directory containing test data)

Executables for Juicebox can be downloaded from http://aidenlab.org/juicebox

The latest command line tools jar can be downloaded from http://aidenlab.org/commandlinetools