Worked Examples

CardamomOT is illustrated on three experimental time-course scRNA-seq datasets, each highlighting different methodological aspects of the package.

Dataset	Organism	Biology	Key feature
Semrau et al. (2017)	Mouse	ESC differentiation (Epi/PE lineages)	In-silico knock-out validation
Kameneva et al. (2021)	Human	Sympathoadrenal lineage development	Multi-lineage branching
Schiebinger et al. (2019)	Mouse	iPSC reprogramming	Non-trivial stimulus schedule

Each example page describes:

• The biological context and dataset characteristics

• The CardamomOT pipeline configuration used

• Key results: inferred network, simulated trajectories, and (where applicable) in-silico perturbations