This repository is solely for educational purposes and serves as a backup for my graduate school assignments related to the BMI 5331: Foundations of Pharmacogenomics course at McWilliams School of Biomedical Informatics at UTHealth Houston.
Folder VCF contains a R script for analyzing Variant Call Format (VCF) files essential for Genome-Wide Association Studies (GWAS), focusing on genotype ploidy, allele phasing, and variant classification, including SNPs, indels, structural variations, and alternative alleles.
Folder Differential_Expression_Letrozole_Responders_vs_Nonresponders contains a R script for the analysis of gene expression between two phenotypes—responders and non-responders to Letrozole drug treatment in the context of breast cancer tumors. The study leverages publicly available microarray dataset from NCBI GEO to identify differentially expressed genes (DEGs) between responders and non-responders.