{"id":20383792,"url":"https://github.com/gmod/jbrowse-jupyter","last_synced_at":"2025-04-12T09:22:05.189Z","repository":{"id":38977094,"uuid":"435633156","full_name":"GMOD/jbrowse-jupyter","owner":"GMOD","description":"A python package for showing JBrowse 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Status](https://img.shields.io/github/actions/workflow/status/GMOD/jbrowse-jupyter/push.yml?branch=main\u0026logo=github)](https://github.com/GMOD/jbrowse-jupyter/actions)\n[![Downloads](https://pepy.tech/badge/jbrowse-jupyter)](https://pepy.tech/project/jbrowse-jupyter)\n\n# JBrowse Jupyter\n\nJBrowse Jupyter is a python package that let's you create JBrowse 2 views in\nJupyter notebooks\n\n## Demos\n\n- Basic usage -\n  [![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)\n- SKBR3 cancer cell line demo -\n  [![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)\n\n## Tutorials\n\n- Tutorial for setting up JupyterLab locally with jbrowse-jupyter\n  https://github.com/GMOD/jbrowse-jupyter-tutorial/\n\n## Documentation\n\nMore documentation here\nhttps://gmod.github.io/jbrowse-jupyter/docs/html/index.html\n\n## Installation\n\n```\n$ pip install jbrowse-jupyter\n```\n\n## Resources\n\n- [JBrowse 2 homepage](https://jbrowse.org/jb2/)\n- [Linear Genome View docs](https://jbrowse.org/storybook/lgv/main/?path=/story/getting-started--page) -\n  storybook docs of React LGV\n- [Dash Applications](https://dash.plotly.com/layout) how to get started to\n  custumize Dash applications.\n- [Dash HTML components](https://dash.plotly.com/dash-html-components) Dash html\n  components to build the Dash application layout.\n- [Dash JBrowse](https://github.com/GMOD/dash_jbrowse) suite of Dash components\n  for JBrowse views\n\n## Contributing\n\nSee our [contributing guide](./CONTRIBUTING.md).\n\n## Citation\n\nJBrowse Jupyter: a Python interface to JBrowse 2, Bioinformatics (2023)\nhttps://doi.org/10.1093/bioinformatics/btad032\n\n## Contact us\n\n- Report a bug or request a feature at\n  https://github.com/GMOD/jbrowse-jupyter/issues\n- Join our developers chat at https://gitter.im/GMOD/jbrowse2\n- Send an email to our mailing list at `gmod-ajax@lists.sourceforge.net`\n\n## FAQ\n\n### What file types are supported?\n\nWe currently support:\n\n- bam/cram\n- bigwig\n- bigbed\n- indexed fasta/bgzip indexed fasta\n- twobit\n- gff3 tabix\n- vcf/vcf tabix\n\n### How do I configure text searching?\n\nIn order to configure text searching in your Linear Genome View, you must first\ncreate a text index. Follow the steps found\n[here](https://jbrowse.org/jb2/docs/quickstart_cli/#indexing-feature-names-for-searching).\nThen you must create and add a text search adapter to your config.\n\n### Can I use local files/my own data?\n\nYes, there are a couple of ways in which you can configure and use your own data\nfrom your local environment in jbrowse views. 1. Make use of the jupyter\nnotebook/lab server. Intended for those running their notebooks with jupyter lab\nor jupyter notebook. 2. Launch your own http server with CORS which will enable\nyou to use local files. You can run our serve.py to launch our dev server.\n(Checkout our local_support.ipynb for tutorials on how to use your own data)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgmod%2Fjbrowse-jupyter","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgmod%2Fjbrowse-jupyter","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgmod%2Fjbrowse-jupyter/lists"}