Fig. 1: Showcase of dyngen functionality.

A Changes in abundance levels are driven strictly by gene regulatory reactions. B The input Gene Regulatory Network (GRN) is defined such that it models a dynamic process of interest. C The reactions define how abundance levels of molecules change at any particular time point. D Firing many reactions can significantly alter the cellular state over time. E dyngen keeps track of the likelihood of a reaction firing during small intervals of time, called the propensity, as well as the actual number of firings. F Similarly, dyngen can also keep track of the regulatory activity of every interaction. G A benchmark of trajectory inference methods has already been performed using the cell state ground-truth²¹. H The cell state ground-truth enables evaluating trajectory alignment methods. I The reaction propensity ground-truth enables evaluating RNA velocity methods. J The cellwise regulatory network ground-truth enables evaluating cell-specific gene regulatory network inference methods.