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Published 20 hours ago • verified publisher icon theislab

Intergrating strategy between AIR and transcriptomics

Open zhouzhendiao opened this issue 2 years ago • 4 comments
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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?

zhouzhendiao avatar Jul 05 '23 05:07 zhouzhendiao

We'll look into this

Zethson avatar Jul 12 '23 08:07 Zethson

We'll look into this

OK, thanks!

zhouzhendiao avatar Jul 12 '23 08:07 zhouzhendiao

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

grst avatar Aug 09 '23 17:08 grst

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.

drEast avatar Aug 29 '23 06:08 drEast