We should update the pipeline to make it even more bulk-specific:
Remove the HVG step, because it's a single-cell-only step
Scaling: The scaling method is called "Seurat", but Seurat is a single-cell package. So maybe we should rename the method like "Simple scaling" or something similar? Only for the bulk pipeline ofc.
In Normalization, can we remove the Log2 method? Also could we add back the DESeq2 method?
In Gene Filtering, can we remove the HVG, Highly Variable Genes, and M3Drop methods? Again, they are single-cell-specific.
In every card and method, it's written "cells: 40" "genes:52030", but it's not cells for bulk, it should be "samples".
In the cards
In the Metadata section. Including when we "Add metadata"
In the Visualization (it's called Cell scatter plot)
We should update the pipeline to make it even more bulk-specific: