Code to reproduce analysis and figures from Xian et al.
The code to reproduce all main figures and tables is in data_preprocessing_main_figure.ipynb
The code to reproduce all supplementary figures and tables is in data_processing_sup_fig.ipynb
The quantification of SCNA score, development of the UPR pathway score, and P53 activity score are avaialble in data_preprocessing.ipynb The differential coexpression analysis is written in R, available in differential_coexpression_analysis_r.ipynb
All data needed to reproduce the results are in the data folder. Note the expression file is too big. Instead, I uploaded the uprDf which contains the UPR genes and RIDD genes fir all TCGA samples required to reproduce the results.