Supporting the analysis of multi-sample SRT data

[Antidington]

Dear author,

Thank you for developing these excellent tools.

I currently have dozens of SRT samples that are unstructured and highly heterogeneous. I would like to know if Giotto is capable of identifying cross-sample gene expression patterns?

Looking forward to your reply!

Best regards,
Jichen

[josschavezf]

Hi @Antidington, yes, the findMarkers_one_vs_all function has the argument cluster_column, you can pass the column containing the sample_id, usually called list_ID to find genes particularly expressed in each sample. Edit: I just realized you may refer to batch effect correction when handling multiple samples. If that's the case, I suggest taking a look to the batch effect correction tutorial: https://drieslab.github.io/Giotto_website/articles/harmony.html