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theislab / scarches

Reference mapping for single-cell genomics
https://docs.scarches.org/en/latest/
BSD 3-Clause "New" or "Revised" License
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example pancreas dataset not there #32

Closed LisaSikkema closed 3 years ago

LisaSikkema commented 3 years ago

Hi! In your example notebook "pancreas_pipeline.ipynb" the file pancreas_normalized_hvg.h5ad is loaded from "./tests/data/pancreas_normalized_hvg.h5ad". However, the file is not there in the repo. Is it possible to upload it again?

LisaSikkema commented 3 years ago

okay seems like the readthedocs is actually more up to date https://scarches.readthedocs.io/en/latest/pancreas_pipeline.html it uses adata = sca.datasets.pancreas() maybe good to update the notebook on the github as well?

M0hammadL commented 3 years ago

hey, we went back to the previous version, now everything should work. The newest version had bugs to we had to remove it.

LisaSikkema commented 3 years ago

okay so I should remove my current scArches and re-install? or are you just talking about the notebook?