This repository provides code to replicate the experiments in the paper "Inferring Cell Differentiation Dynamics with Unobserved Progenitors". Note that it assumes access to a SLURM scheduled cluster.
First clone this repository and initialize the it using
python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt
Then clone TROUPE into a separate directory with
cd ..
git clone https://github.com/raphael-group/troupe.git
and cd into troupe, install as a package, then go back to the experiments directory
cd troupe
pip install -e .
cd ../troupe_experiments
To simulate trees, run the following command:
bash scripts/simulate_trees.sh
To get results for each method run the corresponding cluster script. For example, if you want to run TROUPE, you'd write
bash scripts/troupe/run_cluster_inference.sh