How to remove batch effect when transforming integrated seurat object to monocle2/slingshot?
Hi there,
I have 4 single nucleus RNA-seq data which have batch effect. I used SCTransform workflow to integrate them together. The UMAP result is pretty great. Then I planned to use monocle2 or slingshot for trajectory and pseudotime analysis. I was wondering how to remove the batch effect and creat a trajectory based on my UMAP from seurat? Monocle2 suggests to import count matrix as input and then it does normalizationn finding highly variable features and building up trajectory. But seurat can not return a batch corrected count matrix. Is there anyone who can give me any suggestions and idea? Thanks in advance!
Best, Issac
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