Data processing scripts are included in the respective GEO RNA-seq folders under data directory. These scripts will format the time series data into z-score normalized traning/testing data. And since we are using sequnce data at prior time points to predict expression at later time points, each dataset are then divided to source and target respectively.
To carry out all comparisons between different regression models and to calculate disjoint sets of TFs for different species, use the IPython scripts: network_v_model/*_network_v_model.ipynb. The scripts also output some basic statistic information about the experiments that were presented in the paper
The majority of tables and figures used in the paper were generated through network_v_model/plot_for_paper.ipynb. Additional scripts network_v_model/*_batch_comp.ipynb were used to generate comparisions for batch effects