Welcome to Juicebox!

Software for visualizing data from Hi-C and other proximity mapping experiments

New Features!

In addition to bug fixes and improved streaming speeds, Juicebox 1.4 has many enhancements, including sharing of bookmarks, custom annotating of 2D features, and creating HiC files from your own data!

Command Line Tools

Use command line tools to build your own maps and export data! Check out the documentation and download the latest jar.

Quick Start

Watch this short video for a quick overview of Juicebox!

Open Source

Juicebox has been released Open Source under the MIT License! Fork us on Github!

Juicebox is currently in its beta release. Please contact us if you have questions or bug reports. You can also report bugs via Github Issues.

Citing 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 (In Press).

Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. "A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping." Cell 159, 2014.

* contributed equally