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Intergrating strategy between AIR and transcriptomics #219

Open zhouzhendiao opened 1 year ago

zhouzhendiao commented 1 year ago

Question In chapter Integrating AIR and transcriptomics, the recommended integration is using function scirpy.pp.merge_with_ir, which is remove from scirpy since v0.13. And I noticed scirpy document is using muon rather than scirpy.pp.merge_with_ir. Maybe updating this chapter is necessary to avoid misleading?

Zethson commented 12 months ago

We'll look into this

zhouzhendiao commented 12 months ago

We'll look into this

OK, thanks!

grst commented 11 months ago

There's also some confusion about the outputs not being consistent with scirpy >v0.13: https://github.com/liulab-dfci/TRUST4/issues/96#issuecomment-1661647423

Until the chapter is updated, I suggest to add some warning boxes: https://github.com/theislab/single-cell-best-practices/pull/228

drEast commented 10 months ago

This turns out more difficult than expected as the new Scirpy version is more restrictive in its dependencies and causes some conflicts. But looks do-able. Will keep you updated.