This repository contains a markdown file with the scripts used for the RNA-Seq and ATAC-Seq data analysis performed in the manuscript 'Investigation of the epigenetic effects of phthalates on in vitro thyroid models with RNA-Seq and ATAC-Seq' (Nazzari, M., Romitti, M., Hauser, D., Carvalho, D. J., Giselbrecht, S., Moroni, L., Costagliola, S., & Caiment, F. (2023). Investigation of the effects of phthalates on in vitro thyroid models with RNA-Seq and ATAC-Seq. Frontiers in Endocrinology, 14. https://doi.org/10.3389/fendo.2023.1200211).