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bm2-lab / scMVP

MIT License
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Any tutorial on how to do batch effect correction with this package? #6

Open Chengwei94 opened 2 years ago

Chengwei94 commented 2 years ago

I see that there is a use_batches option in MultiVAE. However, it is not clear to me how I can feed the information of the batches to the model? Is there any tutorial on how to do it? Thanks!

adamtongji commented 2 years ago

Hi, scMVP can automatically remove the batches for datasets from same tech without given known batch labels. We evaluated the performance of batch removal without batch input with replicates of SHARE-seq datasets in our paper. We also found similar performance of batch removal effect with or without known batches using scMVP (not in paper). So we did not utilized this parameter in current demos.

Chengwei94 commented 2 years ago

alright thanks!