livnatje/DIALOGUE

Interfacing with Seurat

Closed this issue · 4 comments

learning-MD commented

Thanks for this really interesting package! I'm looking forward to trying this out. Is there an easy way to interface this with Seurat objects rather than inputting tpm? And, if so, is the the raw counts vs transformed counts (e.g., SCTransform) that should be the input? Thanks!

livnatje commented

Thanks! We will have a Seurat interface/wrapper soon.

As for the input, it is recommended to provide the log-transformed tpm values. If there are specific technical confounders that you think can be mitigated with SCTransform (meaning, regressing those out), then you can certainly use those as well. Keep in mind that you can also provide such confounders to DIALOGUE (conf parameter) instead of regressing those upfront.

wfma commented

Hey any update on this? I am also interested in running Dialogue from Seurat obj but unsure if I am doing it right. I cant find an example of this code to cross check...

Wulin-Tan commented

Hi, any update? I am also longing for the interface with seurat. Thanks.

livnatje commented

Hi @Wulin-Tan, @wfma, and @learning-MD,

A Seurat wrapper and a toy example tutorial showing how to un DIALOGUE with a Seurat object are now provided

I hope this helps.

I'm closing this issue now, but feel free to ask/comment if you have any other questions or issues.

Thanks