A public repository hosting a final script the Lactuca sativa gene regulatory network project I worked on in Richard Morris' lab.
minimise_final corresponds to the Pink et al. 2024 project, and should work, though admittedly needs tidied. The myrchar work corresponds to the paper, "Calcium/Calmodulin-Dependent Protein Kinase Is Negatively and Positively Regulated by Calcium, Providing a Mechanism for Decoding Calcium Responses during Symbiosis Signaling", (Miller et al., 2013), of which I tried to recapitulate the model described of calcium waves in legume root hair nodulation. In short, I did not achieve this, and so neither of those scripts are functioning, however have been uploaded for the records.
Supplementary data can be found in the "Supp_data" file. In that, you may find blockA_up.csv and blockA_down.csv, which represent genes found by OutPredit to be Upstream of the Block A set and downstream of the Block A set respectively.