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xryanglab / SCASL

single-cell clustering based on alternative splicing landscapes
Apache License 2.0
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batch effect removal for multi-sample AS data combination #5

Open wangmeijiao opened 3 months ago

wangmeijiao commented 3 months ago

Hi yang, Here are two quick question: 1) if we want to merge multiple sample of AS single cell data, what strategy do you recommend to use to remove batch effect? 2) the RNA velocity analysis (scVelo, https://scvelo.readthedocs.io/en/stable/) can recapture the potential differential procedure with splicing/unsplicing ratio, however, the splicing data is hard to do batch effect removal. what do you suggest the best way to remove batch effect in velocity matrix?

Best,

Meijiao

ssyshh commented 3 months ago

Hello, your question is very interesting. I would like to ask if you successfully removed batch effects, and at which step did you remove them? How can I use the matrix after batch effect removal to perform UMAP dimensionality reduction and clustering?

thestarocean commented 2 months ago

I also have the same question here regarding the batch effect removal. According to our data, the batch effect seemed to be obvious in splicing landscape between samples.