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CostaLab / scMEGA

scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
https://costalab.github.io/scMEGA
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The use of Co-embedding function #22

Closed LalicJ closed 1 year ago

LalicJ commented 1 year ago

Hi, sorry to bother you. When I run Co-embedding(), I have a question. If I don't ran harmony or other methods on snRNA-seq and snATAC-seq datasets for removing batch effect, what weight.reduction value should I use?

Do you have any suggestions? Any help would be greatly appreciated.

lzj1769 commented 1 year ago

Hi,

You can set weight.reduction as the dimension name used in snATAC-seq, such as LSI, because here we aim to first transfer the gene expression profile from snRNA-seq to snATAC-seq.

Best, Zhijian

LalicJ commented 1 year ago

Thanks! I'll try it.