Open pcarbo opened 1 year ago
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
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?
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)rlang::check_installed
instead of CheckPackage
(3 instances).JoinLayers
before running fastTopics. Best, Sam
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