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: