Files in the Disk:
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0drugdatabase.R: Code to convert data taken from the online TTD database into a standardized R data.frame
0hugoreader.R: Code to convert data taken from the online HGNC database into a standardized R data.frame
0jaincore.R: Code to cluster, illustrate the clustering results, and convert into a standardized R data.frame the results of Jain et al. (2012).
0trimming.R: Contains the custom excise() function used elsewhere in code, finds the first/last specified token in a string and removes all text from the left/right side of the token, including/discluding the token.
1deg1_read_expdata.R: Code to convert gene expression data taken from the online GTEx and TCGA databases into standardized R data.frames and .csv files, the latter for import into MATLAB.
1deg2_limma.R: Code to run variance stabilization and differential expression analyses on gene expression data and visualize the results using MDS plots.
1deg3_make_baseline_and_avgs.R: Code to obtain a gene expression baseline from the healthy gene expression data for import into MATLAB.
2ppi1_constr.R: Code to convert PPI data taken from online databases into an interaction table (readable by Cytoscape) with consistent formatting.
3coexp_wgcna.R: Code to carry out WGCNA on the gene expression datasets.
annotationenrichment: To carry out annotation and enrichment analyses on the clustering data taken from Cytoscape.

chooseObjective.m: An enriched objective function selector for COBRA Toolbox.
doFBA.m: An enriched FBA/FVA function for COBRA Toolbox that carries out these solutions and saves their results to the metabolic model.
doubleSL.m: Adapted from Pratapa (2015), a function that carries out double synthetic lethality experiments on the metabolic model. 
expDatabasePrep.m: Prepares gene expression data for context-specific genome-scale model construction.
findcomparemetnumber.m: Finds and compares between models the total flux through each metabolite.
findExcTbl.m: Turns exchange reaction fluxes into a table.
findOrAddExcs.m: An enriched exchange reaction manipulator for COBRA Toolbox.
findToken.m: Finds which token is used to denote metabolic compartments given a metabolic model. 
getExpRxns.m: Turns gene expression data into "reaction" expression data for context-specific genome-scale model construction.
harmonization.m: Converts arbitrary models into the style of Recon3D.
MAIN.m: Given generic models and gene expression data, creates context specific models, carries out FBA/FVA/flux sampling on the models, and compares outputs.
multTSMbyCutoff.m: Creates multiple tissue specific models using a combination of the INIT/GIMME algorithms by varying their parameters and checking the feasibility of resultant models.
removedDemandBMPC.m: Allows use of COBRA Toolbox's biomassPrecursorCheck() function in models with demand reactions. 
sampling.m: Carries out ACHR sampling to find likely flux distributions
setBounds.m: An enriched exchange reaction bound setter for COBRA Toolbox, discriminating between organic/inorganic nutrients.
singleSL.m: Adapted from Pratapa (2015), a function that carries out single synthetic lethality experiments on the metabolic model. 
visualize_fluxes.m: Visualizes flux distributions of a reaction/multiple reactions, comparing two context-specific models.
visualize_oneside_flux.m: Visualizes flux distributions of a reaction/multiple reactions for only one model.

10419978.pdf: Thesis.
10419978-tezVeriGirisFormu.pdf: Signed scan of the thesis' registration with YOK.

Hardware Requirements:
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Processor: Intel(R) Xeon(R) W-2145 CPU @ 3.70GHz used, however any modern processor is likely sufficient.
Graphics Card: Not required.
Storage: At least 40 GB of storage required for data structures.
RAM: At least 16 GB of RAM required.
Network: Required.
Peripherals: Keyboard, mouse and monitor required. 

Software Requirements:
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OS: Windows 10 Pro x64 used, however any up-to-date operating system is sufficient.
Required Software: COBRA Toolbox 2021, curl, Cytoscape v3.8.0 (and Cytoscape toolbox clusterMaker), Git 2.24.0, Gurobi, MATLAB 2019b, R version 3.6.1 "Action of the Toes" (and R Packages: annotationDbi, BiocManager, biomaRt, clusterProfiler, data.table, DESeq2, DO.db, DOSE, dplyr, edgeR, enrichplot, fgsea, ggplot2, GO.db, limma, org.Hs.eg.db, RColorBrewer, readxl, Rgraphviz, splitstackshape, tidyr, WGCNA), RStudio.