Hi, I have read counts from 10X scRNA Seq data from 3 samples from two different conditions. I want to infer and then compare the inferred regulatory network between the two conditions, for which I am planning to use bigSCal2.
To infer the regulatory network, I am planning to use the read counts from all the 3 samples from a condition (let's say it "A") together to compare it with the rest of the 3 samples from other condition (let's say it "B") together. I am not sure whether it would be the correct approach or should I infer the regulatory network in each sample separately.
I will really appreciate your suggestions.