With the help of GPT-4, I wrote a RMarkdown template for comprehensive exploratory data analysis (EDA). Just get a copy, swap the data and render it. You can also just upload your data to RTutor.ai(https://RTutor.ai) and get a report in minutes.

This R markdown file was auto-generated by the iDEP website (http://ge-lab.org). It is assumed that users have analyzed their data with iDEP by clicking through all the tabs and have downloaded the related files to a folder.

This R Markdown document was generated by by iDEP at http://ge-lab.org/idep/

Just found out that it takes forever to analyze the expression of 25000 genes across 259 samples. I did some investigation on how DESeq2 scales with the number of samples, N. It shows that computing time scales perfectly with O(N^2).

Demos of extracting and interpreting DESeq2 results. Importance of properly setting reference levels for factors.