How to find DE genes between different datasets?

Help scanpy
1

Hi,
I was wondering how you would compare different batches of scRNA-seq data with different celltypes, and get a DE gene list.

I’ve looked through the forums and found a few similar questions but nothing exact for scanpy. I’m just a bit confused because I heard you can’t run DE on batch-integrated data.

Thanks so much!

2

For a primer on differential expression analysis and multi-condition analysis and code examples, I would check out the “Dealing with conditions” chapters of the sc-best-practices book

https://www.sc-best-practices.org/conditions/differential_gene_expression.html