Independent Research Project: Effects of Valproic Acid and Similarity of Gene Expression Changes Compared to Obesity

The owner of this repository would like to thank Dr Marcin Wozniak for writing all of the scripts available in this repository with the exception of analysis_foldAndPathComparison.R and analysis_WCNA.R.

The following files were originally written and supplied by Dr Marcin Wozniak:

1. GEO_datasetsSearch.ipnyb (with substantial modifications/additions done by the owner of this repository)
2. GEO_dataExtraction.ipnyb
3. GEO_rawDataDownload.ipnyb
4. reading_Affymetrix.R
5. reading_NimbleGenIllumina.R
6. analysis_differentialGE.R (with substantial modifications/additions done by the owner of this repository)

analysis_WCNA.R, with substantial modifications/additions done by the owner of this repository, was mostly based on code from "Tutorials for the WGCNA package" by Peter Langfelder and Steve Horvath (https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html), specifically:
"Tutorial for the WGCNA package for R:
I. Network analysis of liver expression data in female mice
1. Data input and cleaning"
(https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-01-dataInput.pdf)
and
"Tutorial for the WGCNA package for R:
I. Network analysis of liver expression data in female mice
2.a Automatic network construction and module detection"
(https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-auto.pdf)

All CSV files used as input in analysis_foldAndPathComparison.R, with the exception of vpa_significant pathway.csv and VPA_gene_set_enrichment.csv, were given by Dr Marcin Wozniak from unpublished materials for use in the project and would not be available via any scripts in this repository.

1. GEO_datasetsSearch.ipnyb
2. GEO_dataExtraction.ipnyb
3. GEO_rawDataDownload.ipnyb

4. reading_Affymetrix.R
5. reading_NimbleGenIllumina.R

6. analysis_differentialGE.R
7. analysis_WCNA.R
8. analysis_foldAndPathComparison.R