search

Teichlab / celltypist

A tool for semi-automatic cell type classification
https://www.celltypist.org/
MIT License
260 stars 40 forks source link

CellTypist with batch correction #31

Closed LeonHafner closed 1 year ago

LeonHafner commented 2 years ago

Hi together, great tool you have created with CellTypist! Since I work with mixed scRNA-Seq data from multiple patients, I need to do a batch effects correction before the cell type annotation. Unfortunately, I don't know of any method that corrects batch effects while leaving the data in a count matrix. There will always be negative data that does not correspond to a count matrix anymore. Is it still possible to apply CellTypist after a batch effects correction, although the data is not in 1e4 and log1p format? Any other ideas to find a workaround for that problem?

Thanks a lot!

ChuanXu1 commented 2 years ago

@LeonHafner, you can resort to your raw count matrices, concatenate them, perform normalization, and apply CellTypist afterwards.