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scverse / pertpy

Perturbation Analysis in the scverse ecosystem.
https://pertpy.readthedocs.io/en/latest/
MIT License
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Add highly variable genes option to perturbation_signature #498

Closed Zethson closed 5 months ago

Zethson commented 5 months ago

Description of feature

Currently it expects highly variable genes as input but doesn't select them from var. We should add a parameter for this.

Zethson commented 5 months ago

It actually uses PCA which already uses highly variable genes if computed.