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mortazavilab / PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad415/7218311
MIT License
209 stars 48 forks source link

single cell data? #44

Closed kunalkathuria closed 1 year ago

kunalkathuria commented 1 year ago

Hi,

I was trying to run PyWGCNA on single cell data (pseudobulk, in the suggested format). I was wondering if there are any downsides to this and if I should try hdWGCNA instead. In particular, our goal is to compare genes in 2 phenotype groups (by trying to run PyWGCNA on each group). Thank you!

Kunal

nargesr commented 1 year ago

Hi,

you only need to make sure all your values are non-negative. Besides that, I believe you should be fine! Feel free to open an issue if you face any problems :)

About your second question, I didn't compare these two packages yet to see how much difference you're gonna see! I would try both packages in your case

kunalkathuria commented 1 year ago

Great, thanks!