using "v2" for SCTransform

[mistrm82]

Replace the code where necessary, add an explanation. And also check that downstream code works well and doesn't change results too drastically

## DO NOT RUN CODE ##

# SCTranform
seurat_phase <- SCTransform(seurat_phase, vars.to.regress = c("mitoRatio"), vst.flavor = "v2")

NOTE: An updated version of SCT "v2" was introduced in early 2022, and is now commonly used. This update improves speed and memory consumption, the stability of parameter estimates, the identification of variable features, and the the ability to perform downstream differential expression analyses. For more information, please see the Seurat vignette.

[mistrm82]

New branch created with SCT-v2 changes to code, homework and downstream analyses. New figurez uploaded too. Still required is new data objects

[mistrm82]

Complete - just needs review: #92