Questions about differential expressed genes

[hiuchi]

Thank you for providing an excellent simulator.

I have started scRNA-seq data analysis, and I have two questions about using this simulator to compare candidate methods for benchmarking.

1. Is there any argument in dyngen::generate_dataset() that is the same as "differentially_expressed_rate" in dyntoy::generate_dataset()?
   Similarly, is "$tde_overall$differentially_expressed" in the output of dyntoy::generate_dataset() not in the output of dyngen::generate_dataset()?

2. We would like to compare the performance of methods for identifying genes that are differentially expressed among lineages.
   In this case, is it reasonable to define HK as negative (genes whose expression does not change between lineages) and TF and target genes as positive (genes whose expression differs between lineages)?

Thank you for your cooperation.