neurogenomics / sckirby Goto Github PK

Saving loom files can be tricky.

Seems like loomR was deprecated in favor of SeuratDisk, so should move all functions over to the latter.

satijalab/seurat#4514

• Seurat
• Signac
• anndata
• SingleCellExperiment
• SummarisedExperiment

https://github.com/scverse/anndataR

https://stuartlab.org/signac/

https://mudata.readthedocs.io/en/latest/

Hey,

Myself and Maria have had issues installing scKirby using conda on the HPC (installing from github after installing all dependencies from it on conda). Might be worthwhile creating a docker image for it? Or if you have a method to use it with conda that would be great to know either.

Thanks!

Seurat::as.Seurat() doesn't know how to convert SummarizedExperiments directly to Seurat objects.
Instead, will have to convert to SingleCellExperiment as an intermediate first.