scMagic2

Vector DB of software tools for scRNA-seq analysis. Demo

How to use

1. Use make_vectordb.py to create and query a vector database of scRNA-esq tools
2. Run steamlit run test_vectordb.py to use vector db as coding recomendatin engine for your scRNA-seq analysis Jupyter Notebook

Some opportunitiy for optimisation

• a clear metric of why it is more usefull then ~gpt-4 is not yet defined
• only tools description and readme files are embedded
• generic embedding model is used

Roadmap

• Get database of scRNA-seq tools and enrich it with tools documentation
• Create vector database of scRNA-seq tools
• Create a simple query engine for vector database
• Create a simple web app to use vector database as coding recomendation engine
• Make web app use vector DB directly
• Make live connection with source data
• Optimise vector DB for scEvals by utisiling citation count, usage context from citations, full documentstion, other metadata, etc.
• Experiment with custom distance metrics, embedding methods and other search/ranking algorithms.

Acknowledgements

• data from scrna-tool.org

Miscelanious

google doc with plan