How I can test my hypothesises computationally
This is what packages like FateID and Monocle are for, namely taking single-cell RNAseq data and inferring differentiation trajectories from it. Don't try to reinvent the wheel on this, there are a number of packages out there to do this sort of thing and they're going to have pretty complicated methods that you're really not going to want to reinvent unless you absolutely have to.