The entire repository is organized into 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
CreateSNPSpecificModel.m: This Matlab code file builds all the QTN-specific models using model extraction algorithms:iMAT, FASTCORE, and INIT by preprocessing the gene-expression data (tpm_counts_Average.csv) using LocalGini or Standep from Yeast genome-scale model (yeastGEM.mat)
--localgini thresholding algorithm can be assessed from https://github.com/NiravBhattLab/Localgini/tree/main
-- The models generated using LocalGini and iMAT are given in the folder.
Deseq2_analysis_up_down.R: This is for differential gene expression analysis
Rif_OOOO_TFs.R: This is for regulatory impact factor analysis