JBrowse Jupyter

JBrowse Jupyter is a python package that let's you create JBrowse 2 views in Jupyter notebooks

Demos

• Basic usage -
• SKBR3 cancer cell line demo -

Tutorials

• Tutorial for setting up JupyterLab locally with jbrowse-jupyter https://github.com/GMOD/jbrowse-jupyter-tutorial/

Documentation

More documentation here https://gmod.github.io/jbrowse-jupyter/docs/html/index.html

Installation

$ pip install jbrowse-jupyter

Resources

• JBrowse 2 homepage
• Linear Genome View docs - storybook docs of React LGV
• Dash Applications how to get started to custumize Dash applications.
• Dash HTML components Dash html components to build the Dash application layout.
• Dash JBrowse suite of Dash components for JBrowse views

Contributing

See our contributing guide.

Citation

JBrowse Jupyter: a Python interface to JBrowse 2, Bioinformatics (2023) https://doi.org/10.1093/bioinformatics/btad032

Contact us

• Report a bug or request a feature at https://github.com/GMOD/jbrowse-jupyter/issues
• Join our developers chat at https://gitter.im/GMOD/jbrowse2
• Send an email to our mailing list at [email protected]

FAQ

What file types are supported?

We currently support:

• bam/cram
• bigwig
• bigbed
• indexed fasta/bgzip indexed fasta
• twobit
• gff3 tabix
• vcf/vcf tabix

How do I configure text searching?

In order to configure text searching in your Linear Genome View, you must first create a text index. Follow the steps found here. Then you must create and add a text search adapter to your config.

Can I use local files/my own data?

Yes, there are a couple of ways in which you can configure and use your own data from your local environment in jbrowse views. 1. Make use of the jupyter notebook/lab server. Intended for those running their notebooks with jupyter lab or jupyter notebook. 2. Launch your own http server with CORS which will enable you to use local files. You can run our serve.py to launch our dev server. (Checkout our local_support.ipynb for tutorials on how to use your own data)