search

SONGDONGYUAN1994 / scDesign3

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
https://songdongyuan1994.github.io/scDesign3/docs/index.html
MIT License
86 stars 24 forks source link

Best way to simulate noise #18

Closed Zethson closed 1 year ago

Zethson commented 1 year ago

Dear developers,

I was wondering whether there's a way to simulate noise for multimodal (CITE, multiome) data. Basically, just a worse fit with more artifacts I guess? I could not find anything in the documentation (from what I've seen).

Thank you very much!

SONGDONGYUAN1994 commented 1 year ago

Hi Lukas, Thank you for your interest in our work! For your question, I think you can modify the fitted parameters to add extra noise (if the noise is defined by yourself, rather than estimated from your data). Specifically, you may check Intro. In the step-by-step mode, extra_para will give you per cell per feature parameters, and you can modify it.

scMerge2 used our method and you may briefly check their design.

Best, Dongyuan

Zethson commented 1 year ago

Great, thank you very much! It's great to also have a connection through @WWXkenmo