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Teichlab / celltypist

A tool for semi-automatic cell type classification
https://www.celltypist.org/
MIT License
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reannotation returns many "UNASSIGNED" cells #71

Closed YawnC closed 1 year ago

YawnC commented 1 year ago

Hi there, I have run into an issue in dataset integration. I used celltypist.harmonize to merge the datasets which were pre-annotated under low-hierarchy. the reannotation result turned to have around 1/3 cells annotated as "UNASSIGNED". Then I tired to annotate each dataset under high-hierarchy, which is like 5-6 basic cell-types per dataset, the "UNASSIGNED“ cells decreased, but still take about 20% of total cells. All these "UNASSIGNED" cells were assigned into certain groups. I wonder whether this is normal, or is there any solutions to further decrease the number of "UNASSIGNED" cells? BTW, thanks for such wonderful tool!

ChuanXu1 commented 1 year ago

@YawnC, you can try the new version (1.5.1 or 1.5.2), which will have fewer UNASSIGNED cells due to an refined reannotation strategy.

YawnC commented 1 year ago

Great! The new version worked with no UNASSIGNED provided! Thanks!