openst 0.1.1

The computational pipeline for the Open-ST method.

Open-ST: open-source spatial transcriptomics

🌐 website | 📜 preprint | 🐁 datasets

Open-ST is an open-source spatial transcriptomics method with efficient whole-transcriptome capture at sub-cellular resolution (0.6 μm) at low cost (<150 Euro library preparation per 12 mm²).

Open-ST requires standard lab equipment and includes open-source software for seamless data processing and analysis.

• Discuss development on GitHub.
• Read the step-by-step protocol.
• Install via pip install openst.

Tutorials and examples

We provide various Open-ST datasets collected by the Rajewsky lab @ MDC Berlin, from various tissues/organisms. There, links to raw and processed data are available, as well as step-by-step guides for (pre)processing and downstream analysis.

Documentation

All the detail to the experimental and computational aspects of our method are available in our website.

We love to have an open approach to documentation. We decided to use mkdocs as our documentation backend to make your life easier. So, feel free to suggest changes by opening a documentation-related issue!

You can build the documentation locally by following these steps:

1. Clone this repository

   git clone https://github.com/rajewsky-lab/openst
   

2. Install the dependencies for building the documentation:

   pip install mkdocs-material mkdocs-autorefs mknotebooks
   

3. Serve mkdocs with the following command:

   mkdocs serve -f openst/mkdocs.yml
   

Contributing

Open-ST is an open-source project mostly maintained by the Rajewsky lab @ MDC Berlin - so, your involvement is warmly welcome! If you're excited to join us, we recommend the following steps:

• Looking for ideas? See our Volunteer Project Board to see what we may need help with.
• Found a bug? Contact an admin in the form of an issue.
• Implement your idea following guidelines set by the official contributing guide
• Wait for admin approval; approval is iterative, but if accepted will belong to the main repository.

In general, you can always refer to the contribution guidelines for more details! Currently, only admins will be merging all accepted changes.

Code of Conduct

Everyone interacting in the Open-ST project's codebases, issue trackers, and discussion forums is expected to follow the PSF Code of Conduct.

License

The software tools of this project are under the GNU License - see the LICENSE file for details.