https://github.com/gmod/jbrowse-jupyter

A python package for showing JBrowse views
https://github.com/gmod/jbrowse-jupyter

genome genome-browser genomics-visualization jbrowse jupyter python

Last synced: about 2 months ago
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A python package for showing JBrowse views

• Host: GitHub
• URL: https://github.com/gmod/jbrowse-jupyter
• Owner: GMOD
• License: apache-2.0
• Created: 2021-12-06T20:10:27.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2024-01-03T16:27:26.000Z (almost 1 year ago)
• Last Synced: 2024-04-10T18:08:38.136Z (9 months ago)
• Topics: genome, genome-browser, genomics-visualization, jbrowse, jupyter, python
• Language: Python
• Homepage:
• Size: 6.45 MB
• Stars: 22
• Watchers: 19
• Forks: 4
• Open Issues: 9
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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# JBrowse Jupyter

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

Jupyter notebooks

## Demos

- Basic usage -

  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GMOD/jbrowse-jupyter/blob/main/examples/basic_usage.ipynb)

- SKBR3 cancer cell line demo -

  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GMOD/jbrowse-jupyter/blob/main/examples/skbr3.ipynb)

## 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](https://jbrowse.org/jb2/)

- [Linear Genome View docs](https://jbrowse.org/storybook/lgv/main/?path=/story/getting-started--page) -

  storybook docs of React LGV

- [Dash Applications](https://dash.plotly.com/layout) how to get started to

  custumize Dash applications.

- [Dash HTML components](https://dash.plotly.com/dash-html-components) Dash html

  components to build the Dash application layout.

- [Dash JBrowse](https://github.com/GMOD/dash_jbrowse) suite of Dash components

  for JBrowse views

## Contributing

See our [contributing guide](./CONTRIBUTING.md).

## 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](https://jbrowse.org/jb2/docs/quickstart_cli/#indexing-feature-names-for-searching).

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)