cell type specific gene regulatory network

[leonardHerault]

Dear all,

Thank you for developing LINGER.

I am trying LINGER with different metacells inputs and I could successfully infer different cell population gene regulatory networks for each of them.

But then, when I try to infer cell type specific GRN from these different inputs I always get the same results...

When reading the code I see that LL_net cell type specific functions load "Primary_TF_TG_chrN.txt" and "Primary_RE_TG_chrN.txt" for the regulatory strengths used in cell type specific GRN inference.

These strength come from the initial provided training on bulk data if I understand correctly.

I thought cell type specific GRN inference use strength inferred from the single-cell training.

Could you please clarify this point?

Best,

LH

[Lau-Jonathan]

Yes, I also encountered this issue. Primary_RE_TG_chrN.txt is used as an input for cell type-specific network inference. It appears that the code for constructing cell type-specific networks using LINGER with cis-reg potential has not been provided