This project creates a simple, easy-to-use web application to visualize complex biological data from single cells. Think of it like a map that helps researchers understand the different types of cells in a sample and how they relate to each other.
Scientists studying cells often use a technique called single-cell RNA sequencing. This generates a lot of data, which can be hard to interpret. This app helps by:
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Uploading Data: You can upload a compressed file (like a zip file) containing the cell data. This data is in a special format called ".h5ad".
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Processing Data: The app takes your uploaded file, unpacks it, and gets the cell data ready for viewing.
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Creating a Visual Map: The app uses a technique called UMAP to create a 2D map of your cells. Cells that are similar to each other will be close together on the map, while different cells will be further apart. This makes it easy to see different cell types and patterns.
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Interactive Exploration: The web application lets you explore this map easily. (Details on how to interact will be provided in the app itself).
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Get the App Running: (Instructions on how to download and run the app will be provided separately).
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Upload Your Data: Once the app is running in your web browser, you'll see a button to upload your zipped cell data file (.zip file containing a .h5ad file).
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View the Map: After you upload the file, the app will process the data and display the UMAP map.
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Explore the Map: You can then interact with the map to zoom in, pan around, and learn more about the different cell groups. (Specific instructions will be in the app).
Imagine trying to understand a city by just looking at a giant list of addresses. It would be very difficult! This app is like creating a map of the city. It takes the complicated cell data and turns it into a visual representation that's much easier to understand. This helps researchers:
- Identify different types of cells
- See how cells are related to each other
- Discover patterns in the data
- Make new discoveries about biology and disease
This app uses some helpful computer tools:
- Shiny for Python: This creates the interactive web interface you see in your browser.
- Scanpy: This tool helps analyze the cell data.
- Matplotlib: This helps create the visual plots.
- Zipfile and OS: These tools help the app handle the uploaded files.
We've tested the app carefully, but sometimes things can go wrong. We've documented some common problems and how to fix them (this documentation will be provided separately). If you encounter a new problem, please let us know so we can improve the app!
By working with this app, you'll learn about:
- Building interactive web apps
- Working with cell data
- Creating visualizations
- Problem-solving and debugging
We hope this app is a useful tool for your research!