✨ Add perturbation use-case

[Zethson]

• Adds a perturbation use-case using McFarland 2020
• Fixes several cleanup cells and missing hide-output tags

[github-actions[bot]]

🚀 Deployed on https://66f2c423c38feb18dc1d77b4--lamin-usecases-ddcd.netlify.app

[sunnyosun]

Could you make this a single cell and hide output? I think the download bar gives a weird whitespace:

[sunnyosun]

Could we have all features lower case, here "DepMap_ID":

[sunnyosun]

Could you put "CRISPRi" instead of "CRISPR"? (in contrast to "CRISPRa" is overexpression)?

Could you call the 2nd type "compound" instead of "drug"? So it's consistent with the registry name

[sunnyosun]

This here is still protein, could you change it to gene please?

[sunnyosun]

I'd suggest:

wl.GeneticTreatment(
    system="CRISPRi",
    name="sgGPX4-1",
)

You can then directly use GeneticTreatment to validate perturbation column:

[sunnyosun]

This is quite long as you are repeating the process 4 times, could we simplify with a loop?

[sunnyosun]

Is it possible to map out the compound names manually? Relying on search here feels quite hacky:

[Zethson]

Is it possible to map out the compound names manually? Relying on search here feels quite hacky:

Required renaming a compound which got created using a synonym in the data because else .get(name="bla") would not find it. search() results in less code but .get() is less hacky.