# 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)](semrau.md) | Mouse | ESC differentiation (Epi/PE lineages) | In-silico knock-out validation |
| [Kameneva et al. (2021)](kameneva.md) | Human | Sympathoadrenal lineage development | Multi-lineage branching |
| [Schiebinger et al. (2019)](schiebinger.md) | 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