The Effect of Antibiotic Treatment on the Expression of Antibiotic Resistance Genes in the Intestinal Microbiome

This was my final project for Biomedical Data Science class, an elective I took while I was a 3rd year student at the University of Virginia (in spring 2020). The project required us to pick a topic of interest, identify a publicly availble genetic sequencing dataset that is relevent to our topic, and develop and carry out a processing pipeline in order to test our hypothesis. I chose to investigate the expression of antibiotic resistance genes in the gut microbiome.

Much of the data processing was done on UVA's high performance cluster, and as such the pipeline cannot be run from the beggining by cloning this repo. Instead, the repo contains preprocessed data that was exported after running the first part of the pipeline. R is used to run statistical tests and plot this data for the final report.

The final output of the project can be seen by downloading FinalReport.html