sc-eVIP formula + implementation

[gwaybio]

Hi @oursu , thanks for making this repo public!

I am in the process of benchmarking a new metric (see https://github.com/broadinstitute/grit-benchmark) and would like to include eVIP as a comparison. However, I cannot seem to find the implementation! Am I not looking in the right place? If you could point me in the right direction, that would be great.

Thanks!
Greg

[gwaybio]

(it might also be important to note that I want to compare grit to eVIP and sc-eVIP)

[oursu-broad]

Hi Greg!

I am in the process of making an easy to use script for running sc-eVIP. I will only get to it in the weekend. In the meantime, you can check out the notebooks that say "scoring" (e.g. https://github.com/klarman-cell-observatory/sc_eVIP/blob/master/2020-07-09/2020-09-15_iii.TP53_scoring.ipynb) and you can find the code I used there. Or you can wait for me to post a wrapper at the end of the week.

Best,
Oana

[gwaybio]

Thanks Oana!

It looks like the function doing the heavy lifting is compare_2_groups_df() in that script. I think a wrapper would also be helpful. I'll be on the lookout!

I also thought that it might be worth pointing you to an additional option, in case you are interested: the Imaging Platform is writing software to quickly evaluate profile quality (see https://github.com/cytomining/cytominer-eval). We are actively developing the python package now, and would welcome eVIP with open arms. It will definitely require more work to add the function (adding tests, incorporating into existing API, etc.), but it is stable and user-friendly.

Best,
Greg