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azizilab / DIISCO_public

Publically accessible code for DIISCO method
MIT License
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how to run DIISCO in single cell data, which notebook i should to start first? #6

Open tian6067 opened 1 month ago

tian6067 commented 1 month ago

Hi,

This toolkit is excellent! Forgive me, I'm a newbie.

I want to use it in my own single cell dataset (scanpy dataset). but which one in nootbokhttps://github.com/azizilab/DIISCO_public/tree/main/notebooks, i should start first, because i don't found the scanpy dataset as input to DIISCO. so is the gene experssion matrix (csv) as input?

please tell me, thank you very much.

cameronyoungpark commented 1 month ago

The input to DIISCO is cell type proportions over time. Your single cell dataset needs to have samples sequenced at multiple time points and you need to go through your preferred clustering/annotation pipeline. The gene expression is only used in generating the prior and in post processing to predict R-L interactions. We are currently updating the package so please check back in a few weeks!