This file contains list of code files and their description. Most code files have multiple sections, listed in the header of the file with their description. 

>> QCpipelineBSC.m
pre-processing of the brain snuc-RNAseq data, includes QC and generating of the .mat expression data files from this data. There are different groups of analyses and versions of processed data. 

>> clusteringComparison.m
General study of the network clusters (from GTEx-cortex data) and comparisons. Some major plots are here as well. 

>> GTEx_cellTypeCorrection.m
This file has multiple components. It is mostly focused on correcting the bulk GTEx-brain-cortex dataset. The correction is performed with different lists of markers, as well as random lists of genes.

>> corrCluster_function_GTExExpGenes.m
This is a funciton for clustering the given list of genes in GTEx_brain_cortex data. 

>> markerIdentificationInSC.m
Code for identification of marker genes in the snuc-RNAseq data. 

>> moduleRepresentation.m
Code for enrichment of functional terms in different networks. 

>> buildingNetworks_GTEx_SC.m
Code for building binary networks from GTEx datasets and snuc-RNAseq cell populations. 

>> networkOverlapLR.m
Getting the overlap between all networks, snuc-RNAseq and GTEx included. 

>> gettingTheTSSDistForBiPrimer.m
In this file I extract the highly represented links (repeated in multiple snuc-RNAseq networks). I also examine various reasons explanining their recurrence - such as bidirectional primers etc. 

>> overlappingLinks_SC.m
A file for studying and plotting the overlapping links among snuc-RNAseq networks. No major data files are generated in this file. 

>> generateBulkFromSC.m
Here I generate the simulated bulk datasets from snuc-RNAseq data. 

>> specificResults.m
Some final plots and text result files included in the manuscript are made in this file. 

>> simCorrOfCTPVar.m
This has the simulation code in the supplement and some experiments and plots regarding the simulation. 

>> clusterMyGenes.m
Code for clustering the networks. 

>> bloodRun.m
This has all the code for blood analysis - most parts are copied from brain analysis.





