integrating snRNA (from multiome dataset) with scRNA public dataset

immunogenomics / harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

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integrating snRNA (from multiome dataset) with scRNA public dataset #258

Open Urja25 opened 2 months ago

Urja25 commented 2 months ago

Hi,

I tried integrating three PBMC snRNAseq data from 10X Genomics multiome datasets with two scRNA seq data from a 10X Genomics Public dataset. However, all the data from the multiome clusters separately from the scRNAseq data. How can I remove batch effects in this case?

Thanks a lot!

pati-ni commented 1 month ago

Are you using only snRNAseq? Is everything PBMC? Can you provide a walkthrough of your analysis?