How to integrate multiple single cell RNA-seq samples and perform pseudotime analysis by Monocle2
Hi there,
I have 3 single cell RNA-seq samples and I would like to perform pseudotime analysis using Monocle2. I integrated these 3 samples together and normalized the merged dataset by SCTransform method with Seurat3 package. But this data can not be imported in Monocle2 cause the author said not normalize data yourself. I was wondering how to handle this case. Can Monocle2 remove batch effect just using log-transform and scale function? Thanks in advance for any suggestions and advices!
Best, Issac
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