Changing the code to SCT to include "v2" results in small differences downstream, and the celltype to cluster mapping changes slightly. As such many things have been updated here including:
all images after SCT (since it is a new UMAP)
code mostly in marker identification
content and flow in marker identification to match the new clusters
Also, I have created a new download with a new seurat integrated file and I have updated the "workshop_data" folder with all new RData files and scripts to match v2. This should be complete - but could use a review!
Changing the code to SCT to include "v2" results in small differences downstream, and the celltype to cluster mapping changes slightly. As such many things have been updated here including:
Also, I have created a new download with a new seurat integrated file and I have updated the "workshop_data" folder with all new RData files and scripts to match v2. This should be complete - but could use a review!