Welcome to the workshop webpage for Research Approaches II: Data Analysis (course: Research Trends in Toxicology (mi8016)). This hands-on workshop reproduces the statistics and figures from two toxicology papers investigating PFOS:
- Figure 1F and figure 3 from paper PFOS induces proliferation, cell-cycle progression, and malignant phenotype in human breast epithelial cells, 2018 (PFOS phenotype paper).
- Figures 1 and figure 3 from paper Perfluorooctanesulfonic acid (PFOS) induced cancer related DNA methylation alterations in human breast cells: A whole genome methylome study, 2024 (PFOS EM-seq paper).
Important
This workshop is ran in R! No previous experience with R or bioinformatic data analysis is required.
If you are new to R, follow this tutorial Introduction to R. Make sure you go through this tutorial before the workshop.
Workshop parts
- Introduction to R: How to install R and some basic commands to get you started
- T-test: Here we reproduce the statistics and make a figure which shows the cell migration and cell invasion after 10µM PFOS exposure.
- ANOVA: Here we reproduce the statistics and make a figure which shows the proliferation over mulitple doses of PFOS.
- Methylome Analysis: Here we reproduce figures showing descriptive statistics and gene ontology results after 1µM PFOS exposure.