Digital Epidemiology and Precision Medicine -- Final Project

This is a Github repository created to submit the final project of the Digital Epidemiology and Precision Medicine course for the MSc. in Data Science at the Sapienza University of Rome.

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What's inside this repository?

1. README.md: A markdown file that explains the content of the repository.

2. script/: A folder including 4 R scripts used to perform the analysis for the report. The files included are:

   • deg_data_preprocessing.R: An R script to preprocess TGCA data in order to obtain the Differentially Expressed Genes (DEGs).

   • co_exp_net.R: An R script to obtain gene co-expression networks and differential co-expression networks for cancerous and healthy samples. The objective was to characterize hubs and scale-free behavior.

   • ps_net.R: An R script to obtain patient similarity networks with gene expression and mutational profiles and perform PSN and Survival Analysis to characterize clusters of patients.

   • enrichment_analysis.py: An R script to perform Gene Set Enrichment Analysis to the hub genes found in previous analysis.

3. data/: A folder containing intermediate data used for running the scripts above.

4. figures/: A folder containing the figures obtained given the analysis.

5. .gitignore: A predetermined .gitignore file that tells Git which files or folders to ignore in an R project.

6. LICENSE: A file containing an MIT permissive license.

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