Using scMEGA for two treatment groups?

[klgoss]

Thanks for creating this wonderful tool! In the vignettes, you add the trajectory before selecting TFs. In my case, I'm not as interested in comparing between cell types but rather a control and treated group. Is this possible and if so, how would I go about doing that? Am I able to skip the trajectory step?

[lzj1769]

Hi @klgoss

Sure, you can skip the trajectory analysis if there is a way to select candidate TFs, for example, by performing differential analysis using TF activity as estimated by chromVAR.

But since we developed this package for inferring GRN from cells that form a trajectory, I am not sure how the results will look like when applied to two groups.

Best, Zhijian

[igcf]

Dear all,

Indeed, scMEGA was not defined to look at two conditions, but one possibility to explore this would be to run it on an integrated data (ignoring conditions). You could then at the regulatory network level try to relate nodes (TFs or genes) to conditions by using differential TF activity and gene expression analysis.

best, Ivan

Em qua., 8 de fev. de 2023 às 21:01, Zhijian Li @.***> escreveu:

Hi @klgoss https://github.com/klgoss

Sure, you can skip the trajectory analysis if there is a way to select candidate TFs, for example, by performing differential analysis using TF activity as estimated by chromVAR.

But since we developed this package for inferring GRN from cells that form a trajectory, I am not sure how the results will look like when applied to two groups.

Best, Zhijian

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