Suggestions for DE analysis

[grst]

1. use decoupler

I think a few sections of the DE section could be cleaned up by using decoupler functions instead of custom ones:

• decoupler already has a function to compute pseudobulk: get_pseudobulk
• decoupler also has a function to make volcano plots: plot_volcano.

2. additional visualization ideas

I have used some additional approaches for visualizing DE results in the past. Let me know if you are interested:

• paired or unpaired scatter+boxplots are nice ways of visualizing individual genes (each dot is a pseudobulk-sample)

• barcharts with scatterplot for paired observations (bar = mean fold change, dots = fold changes for all paired observations) is a nice way of visualzing top N results.