I find one small mistake in your source code, please check it.

[mingze-yuan]

There is one small mistake in your source code of simulate_counts.R.

• In function SimulateVeloCycle, the 455th line should be return(list(counts_u = result$counts_u, counts_s=result$counts_s, kinet_params=final_kinetics, state_mat=result$state_mat, cell_time=result$cell_time, velocity=result$velocity, dynamics=dynamics, backbone = evf_res[[2]]$pop, chosen_hge = chosen_hge)), you mistook counts_s=result$counts_s as counts_s=result$counts_u.
• The same mistake is also in the 577th line.
  Thanks for you package, this helps me a lot! Please check it.

[PeterZZQ]

Thank you. Have updated it, and it should be correct now.