Starlitnightly / omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
https://starlitnightly.github.io/omicverse/
GNU General Public License v3.0
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`sccomposite` filtered out almost half number of my cells. #155

Closed colinwxl closed 1 month ago

colinwxl commented 1 month ago

Is it reasonable that sccomposite filter out almost half of the number of my cells. I have used sccomposite in ov.pp.qc with a batch_key='sample', and found out most of the cells was filtered out, which superized me a lot. QQ20240919-074856

Starlitnightly commented 1 month ago

That's surprising, but you can also manually check the data quality, after all, algorithms aren't perfect.