Is there any possibility to have this tool work with scRNA-seq data?

[GilbertHan1011]

Hello, thanks for providing such an amazing tools!

I noticed this tool is available for bulk RNA data. But since the scRNA-seq data is much more large and sparse, I don't know whether it can work with scRNA-seq data. And for a more complex situation, I identify differential genes with trajectory inference method, which means there is no literally group/condition at all, what should I do to deal with this situation.

I'd be more than grateful if you can answer my question!

[noriakis]

Dear @GilbertHan1011,

Thank you very much for your important suggestion. I apologize for the delayed response.

As you stated, scRNA-seq data is currently not supported, but need to be supported. The consideration for sparsity and high dimensionality is indeed necessary I think, and some packages performing the inference of Bayesian network for this specific purpose are developed. I will try to implement this feature by piping these packages in the future.

Regarding the differential genes identified by the trajectory inference method, I don't have a lot of experience with this type of analysis, but one option would be performing enrichment analysis (EA) by differential genes that change along the trajectory, and subsequently performing inference of dynamic GRN by like DBN, based on the ordering of clusters and EA result, although this would be computationally intensive.

I will try to see if such an implementation is possible and would appreciate it if you could share any ideas you come up with.