Tutorials on linear models, mixed models, hierarchical models etc. for gene/protein expression

Question

[The]

Hello All,

I'm looking for some tutorials on application of linear models , mixed models, hierarchical models etc. on gene or protein expression studies. Particularly how to use these statistical models to find out deferentially expressed genes and proteins.

I'm looking for simple worked out examples (toy models would do) which don't use software packages like "limma" and preferably in R or Python. I've no qualms against limma , but for me I've to delve a lot I guess to look into what actually happening inside limma or other similar packages.

Suggestions on any book, tutorial , website, Jupyter or other notebooks which got worked out examples are most welcome.

Thanks