HiC contact matrix visualization

View the Project on GitHub

juicebox.js is an embeddable interactive contact map viewer for .hic files written in JavaScript and CSS. It is based on the desktop Juicebox visualization application. For developers who wish to embed juicebox.js, see the Developer Documentation

A public juicebox.js instance can be found at http://aidenlab.org/juicebox.

aidenlab.org/juicebox: Quick Start Guide

Begin by loading a contact map (hic) file using Load Contact Map > Select Contact Map. The menu list is searchable. The viewer will initially open on the first chromosome in the file on both axes of the map display.

Navigate to locus

Pan and zoom

Change resolution

Contact Map Color Scale


Load Local File or by URL

In addition to the provided menus, .hic contact map files and track files can also be loaded from the local file system or by URL. All common genomic track file formats are supported (bigwig, begbed, wig bedgraph, bed, gff3, and gtf). The supported 2D annotation format is described in the desktop Juicebox documentation.

Multiple Maps

View and compare two or more maps. Click on the + button above the map panel to create a new empty panel, and load another contact map. Note that all maps must be based on the same genome assembly.

Sharing Your Maps

The visualization state can be captured and shared by using the Share button. The generated URLs encapsulate the current state of the application with the exception of locally loaded files (that is, files loaded from the user’s local file system). Files shared via juicebox URLs can be public or private, and can be shared with anyone who has access to the files. The URLs do not have an expiration date.