Updated compatibility for Seurat

[aliibarry]

Minor updates to work with Seurat V5, addressing depreciation of slot for layer as discussed in #133

Includes additional switch from tsne to umap default when running basicSeuratProc(); although I never debugged why tsne fails with some Seurat V5 objects.

[evanbiederstedt]

Thanks @aliibarry

So, basically everything works except the Seurat developers deprecated 'slot' for 'layer' ? This is for Seurat V3 as well?

It's been a while since I have looked at the v5 Seurat tutorials.

I suspect you are just running this guide, right? https://satijalab.org/seurat/articles/seurat5_integration

Question:
Is there anything else you are doing with Seurat and Conos? I'll try to debug + to check if this works.

Question:

Includes additional switch from tsne to umap default when running basicSeuratProc(); although I never debugged why tsne fails with some Seurat V5 objects.

You could provide more details/outputs? That would be helpful for me to debug.

Best, Evan