Construct GAM without RNA velocity

[siefejo1]

... Thanks for the great program! I am using the CytoTRACEKernel to run Cellrank functions in the absence of RNA velocity. Is it possible to construct a GAM from this transition matrix?

[michalk8]

Hi @siefejo1 , yes, absolutely, there's no need for RNA velocity, just for a pseudotime (you can use the CT pseudotime for example); see the time_key argument in e.g. GAMR.prepare.

[siefejo1]

Got it. With regards to determining the terminal states and lineages first, if I run the GPCCA estimator on a combined kernel of CytoTRACEKernel and ConnectivityKernel, will that update the adata object with the necessary parameters for the GAM?

[michalk8]

Got it. With regards to determining the terminal states and lineages first, if I run the GPCCA estimator on a combined kernel of CytoTRACEKernel and ConnectivityKernel, will that update the adata object with the necessary parameters for the GAM?

Yes, it should be updated so that all data needed for GAM fitting is there.

[Marius1311]

I'm closing this, it looks solved.