# Juicebox

## Juicebox

- [Welcome!](https://aidenlab.gitbook.io/juicebox/master.md)
- [Background](https://aidenlab.gitbook.io/juicebox/background.md): Background of 3D Genomics and Hi-C Data
- [Juicebox (Web)](https://aidenlab.gitbook.io/juicebox/juicebox-web.md)
- [Loading Annotations (Web)](https://aidenlab.gitbook.io/juicebox/loading-annotations-web.md)
- [Comparing Maps (Web)](https://aidenlab.gitbook.io/juicebox/comparing-maps-web.md)
- [Sharing URLs (Web)](https://aidenlab.gitbook.io/juicebox/sharing-urls.md)
- [Hosting with Dropbox/Drive/GEO](https://aidenlab.gitbook.io/juicebox/hosting-with-dropbox.md)
- [Visualize from ENCODE website](https://aidenlab.gitbook.io/juicebox/visualize-from-encode-website.md)
- [Practice: Interactive Figure](https://aidenlab.gitbook.io/juicebox/interactive-figure.md)
- [Juicebox (Desktop)](https://aidenlab.gitbook.io/juicebox/desktop.md)
- [Loading Annotations (Desktop)](https://aidenlab.gitbook.io/juicebox/loading-annotations.md)
- [Comparing Maps (Desktop)](https://aidenlab.gitbook.io/juicebox/comparing-maps.md)
- [Drawing Custom Annotations (Desktop)](https://aidenlab.gitbook.io/juicebox/drawing-custom-annotations.md)
- [Additional Resources](https://aidenlab.gitbook.io/juicebox/additional-resources.md)
- [Bonus: Running Juicer Tools Analysis](https://aidenlab.gitbook.io/juicebox/bonus-running-juicer-tools-analysis.md)
- [Bonus: Accessing Raw Data for Analysis](https://aidenlab.gitbook.io/juicebox/accessing-raw-data.md)
- [Bonus: Assembly Tools (Desktop)](https://aidenlab.gitbook.io/juicebox/assembly-tools.md)
- [Bonus: Submapping (Desktop)](https://aidenlab.gitbook.io/juicebox/submapping.md)