Hi,

I am planning to merge four independent scRNA-seq dataset to analyze. Two of these are public datasets from NCBI GEO and the rests are our own datasets. I basically follow the Seurat pipeline (https://satijalab.org/seurat/articles/integration_introduction.html).

My question is how to verify the effects of merging? Such as whether to get rid of batch effects.

Furthermore, do you have other excellent methods to integrate scRNA-seq dataset?

Thanks