harmony

[Flu09]

General question. I am working on several datasets that have been already integrated by harmony. I am wondering if scvelo will work on such integrated object? or if you have recommendations on the integration method preceding the use of scvelo?

[jjia1]

I don't see why it would cause any problems. Harmony is only used for batch correction and generates a new set of PCs that are supposed to reduce batch effects. If you don't actually end up using the harmony PCs, then I can't see it causing any problems. Even if you do use those PCs, I don't see why it would cause any issues as it should be better than using PCs generated from regular PCA.