This code is in adjunct to the paper linked below.
Satwik Pasani; Sarthak Sahoo; Mohit Kumar Jolly; Hybrid E/M phenotype(s) and stemness: a mechanistic connection embedded in network topology, 2020
The raw_data zip file must be extracted first. It contains a nested folder organization according to the circuit and the level of expression (i.e. overexpression (oe10), downexpression (de10) or unperturbed (oe0)). Each final folder has the 5 .topo files for the 5 replicates of the circuit (except the uncoupled circuit), with one scriptfile_all.sh file per folder containing the bash script to run RACIPE on all the .topo files in the folder. The terminal outputs of the 5 runs, as evident from the bash script, is stored in the termoutput files. The actual outputted files are not included due to their large size.
The remaining files are the python scripts to reproduce the tables/figures created in the analysis. Before running, two empty folders titled collated_data and figures must be created in the working directory. figures must contain the subfolders plots and tables_numbers and clustering. The order in which the scripts must ideally be run is as follows: collate_data -> normalize_data -> cluster_data -> tables_and_numbers_1/2/3 -> statistical_significance_1/2 -> figures_1/2/3/misc -> additional_analysis/2