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emdann / milopy

Python implementation of Milo for differential abundance testing on KNN graph
MIT License
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Where can I find the information about to which neighborhood a cell belongs #29

Closed ZhenjiangFan closed 1 year ago

ZhenjiangFan commented 2 years ago

Thank you for your amazing work.

I am trying to use your method to group all the cells of a single-cell dataset into neighborhoods or clusters. However, I could not find any information about to which neighborhood or cluster a cell belongs after running Milopy. It would be great if you would tell me how to find this information.

Thank you.

Fan

emdann commented 2 years ago

Hi @ZhenjiangFan, thanks for using milopy. You can find the assignment of cells to neighbourhoods in adata.obsm['nhoods'] (made after running milopy.core.make_nhoods)

ZhenjiangFan commented 1 year ago

Sorry that I forgot to respond to your message. Thank you Emma for your time. I appreciate it.