Seurat- SCTransform compatibility? about swne HOT 4 CLOSED

Hi! Sorry for the late reply, was working on a manuscript deadline. Thanks for pointing this out, I've updated the RunSWNE function to look for object@graphs$SCT_nn when the DefaultAssay is SCT, which it is automatically set to after running SCTransform. Let me know if that works!

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Hi, thank you! I forgot about this but just tried it again today and it works flawlessly now!

Just another suggestion: in your Readme, maybe recommend remotes::install_github() instead of devtools::install_github(), the former has much less dependencies and often work where the latter gives errors.

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Thanks for the suggestion, I just updated to using remotes! Yeah I've noticed devtools does not handle dependencies well too

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Hi @yanwu2014, apologies for the mistake, I double checked and realised it's remotes::install_github(), not remotes::install()

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