openpipelines-bio / openpipeline

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Generate scGPT zero-shot cell type annotation module #772

Open dorien-er opened 1 month ago

dorien-er commented 1 month ago

Conversion of src/scgpt/annotation/script.py into a viash component (script is available from branch scgpt-annotation)

dorien-er commented 1 month ago

This script is based on the following scGPT tutorial, but we factored out the training aspects and just do zero-shot inference instead.

https://scgpt.readthedocs.io/en/latest/tutorial_annotation.html