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calico / scBasset

Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
Apache License 2.0
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batch correction scBassset-BC #6

Closed willey2020 closed 2 years ago

willey2020 commented 2 years ago

Hello! Could I ask if the scBasset-BC method is in this repo? My data has strong batch effect with 2 assays. is it possible to try BC with scBasset? Thank you!

willey2020 commented 2 years ago

I found def make_model_bc() I guess this is for the batch correction. Could I ask if there is a short tutorial for it, thank you so much!

hy395 commented 2 years ago

Hi,

Yes, make_model_bc() is for batch correction. There's a bin/scbasset_bc_train.py file for training. And for extracting cell embeddings, imputation, and TF activity inference, there is a bc option which indicate whether the model is trained as scBasset-BC or not. Sure, I'm happy to upload a tutorial for batch correction shortly (today or tomorrow). I'll give you an update then.

willey2020 commented 2 years ago

Thank you so much!!

hy395 commented 2 years ago

Hi, I just updated the repo, added a very simple tutorial on how to run scBasset-BC. Hope this can already get you started. I'll add more evaluation later.

willey2020 commented 2 years ago

Thank you so much again! It is super clear and very helpful! I will try it with my batched data. Thank you again for making this great architecture and analysis method!