Ground truth expression trends for mol_mrna in different cell lineages

[spriyansh]

How can we elucidate the ground truth for the mol_mrna from the dyngen object?

I am following the tutorial here.

Following code prints out the expression trends for the gold standard

plot_gold_expression(model, what = "mol_mrna") # mrna

Is there a way to plot the expression of a single mol_mrna throughout all the cell states/lineages? I want to examine how a particular mol_mrna changes its expression trends in different lineages.

[spriyansh]

Hi @rcannood and @zouter,

Do you have any updates on how to look for the actual expression of genes across lineages in pseudotime? I want to use this information as a ground truth for the differential expression method. For example, Splatter provides a table with fold changes, using which we can infer which gene is differentially expressed in which lineage.

Is something like this available in Dyngen? Using the GRN (model$feature_network), I can only look for TF modules, but what about the expression trends of Target genes? How can we know the actual expression of them?