The entire repository is organised in two folders:
- metabolic-modelling-of-SPO-QTNs
- RNA_seq-analysis
The folder QTN_specific_metabolic_models has all the QTN-specific metabolic models built in this study
Description of other files
QTN_specific_model_building.m: This matlab code file builds all the QTN-specific models used in this study using the gene-expression data (tpm_counts_Average.csv) and the Yeast genome-scale model (yeastGEM.mat)
optgp_sampling.ipynb: This notebook is for sampling analyis and data vizualisation
Deseq2_analysis_up_down.R: This is for differential gene expression analysis
Rif_OOOO_TFs.R: This is for regulatory impact factor analysis