To replicate the simulation experiments described in the paper:

1. Install the required packages listed in requirements.txt (eg. pip3 install -r requirements.txt), ensure directory is added to PYTHONPATH
2. Run simulation_experiments/run_experiments.py
3. Plot the results with simulation_experiments/plot_results.py


To replicate the gene expression experiments (additional helper scripts to be added for preprocessing):
1. Install scanpy
2. Preprocess the gtex gene expression data as described in the paper, add result to gene_expression_experiments/data
3. Extract the list of TF and target pairs from HFtarget, save the python dict as a pickle file in gene_expression_experiments/data
4. Run either run_mcc_experiments.py or run_transfer_test_experiments.py and the corresponding plotting file in gene_expression_experiments