fastTopics wrapper

[pcarbo]

Dear Seurat Developers,

I'm submitting for your consideration a simple Seurat wrapper for the fastTopics package.

The most recent methods are described in a bioRxiv preprint.

I tried to follow the "contribution guide", but please let me know if you would like me to make any changes to the interface or implementation.

Thank you,
Peter

[pcarbo]

Hi Seurat Developers,

The paper describing these methods is now published in Genome Biology.

Please let me know if I should update the fastTopics wrapper code to address any new requirements or compatibility issues with the latest version of Seurat.

Thank you!
Peter

[pcarbo]

Hi, now that Seurat 5 is released on CRAN, would now be a good time to revisit this pull request?

Should I make sure that this wrapper is compatible with Seurat 5, and update it as needed?

[samuel-marsh]

Just adding a +1 in support of Seurat5 support and +1 to Seurat Team in terms of merging into SeuratWrappers.

@pcarbo in terms of updating to Seurat 5 it's pretty straightforward (from my brief testing). Only changes I had to make were:

• LayerData instead of GetAssayData. (Line 447)
• Use rlang::check_installed instead of CheckPackage (3 instances).
• Depending on how you want users to be able to use it either add support for individual layers or add a check to require users to run JoinLayers before running fastTopics.

Best,
Sam