Update integrations.R

[shivangsharma]

Replace NormalizeData(), FindVariableFeatures() and ScaleData() with SCTransform()

[evanbiederstedt]

@shivangsharma Thanks for this. I appreciate the help.

This function was originally written to work with Seurat V3.

I wonder if it would make sense to create a Seurat V5 function. There's a related discussion here, but we didn't get a response from the Seurat team : #133

I haven't had the bandwidth to check for all of the changes for V5.

Are there other changes recommended here? Have you successfully tried running these functions with Seurat V5?

Best, Evan

[shivangsharma]

Hi Evan,

That's a great question. I've been using Seurat v5 for a while and can see that multiple changes need to be made into the conos package (wherever Seurat is used). However, SCTransform() provides an improvement over ScaleData() when using Harmony. So, I'm excited to see if the same is observed for Conos as well. Currently, I'm trying to make whatever changes I feel would be necessary into my fork of conos.

[evanbiederstedt]

Thanks for the help with this @shivangsharma
You're doing invaluable work.

How about the following plan:
Would you make Seurat V5 changes to the above using this PR? Let's convert this PR (Pull Request) into a Draft PR, and when you're ready, please make change it back to an "official" PR and ping Viktor + myself for a review.

Would that be a reasonable way forward? In the meantime, please keep pushing commits to this branch.

I really appreciate the help; someone should do this, but we don't have the bandwidth here.

Thank you!

[shivangsharma]

I agree @evanbiederstedt , its a much needed step. The plan sounds good. I'll keep pushing commits to the brach with changes. Meanwhile, if I have some questions about code snippets, I'll keep posting them here.

I've changed the PR to draft PR. Also, please let me know if someone else is also working on this and we can collaborate.

Thanks for the suggestions,
Shivang

[VPetukhov]

@shivangsharma , thank you for the PR! I think we're fine with dropping Seurat 3 support and switching to v5.