Batch correction in expression space data set unavailable

theislab / cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

BSD 3-Clause "New" or "Revised" License

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Batch correction in expression space data set unavailable #52

Closed fabi-lab closed 6 days ago

fabi-lab commented 3 weeks ago

Hello,

I am trying to reproduce the results from the [Batch_correction_in_expression_space.ipynb] file but it appears that the data set cannot be downloaded using the presented Google Drive link.

Can I receive an updated link?

Thanks in advance, Fabi

ArianAmani commented 6 days ago

Hi Fabi, thanks for your interest in CPA. Thanks for letting us know, I will update the notebook asap with the new link to the dataset, but in the meantime, you can download the dataset from the original source using:

!wget --content-disposition https://figshare.com/ndownloader/files/25717328
adata = sc.read('Immune_ALL_human.h5ad')