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Non overlapping scRNAseq reference data #12

Open KaBach opened 4 years ago

KaBach commented 4 years ago

Hi

I was wondering whether the reference data sets need to be completley overlapping in terms of identified cell types? Or is it possible to have a certain cell type only represented in one data set but not in another?

Best Karsten

meichendong commented 4 years ago

Hi Karsten, Thanks for using SCDC! This is a good question. Currently, the ENSEMBLE function needs the input reference datasets to have overlapped cell types. In your case, if you have reference data of different cell types from different sources, would you know why some major data types are missing in one or more datasets? You might want to consider using some batch correction methods to put all the reference data together.