Xijin Ge

Recently Published

Exploratory data analysis, automated
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 and get a report in minutes.
Reproducing iDEP analyses with auto-generated R Markdown
This R markdown file was auto-generated by the iDEP website ( 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.
R Markdown for iDEP
This R Markdown document was generated by by iDEP at
DESeq2 computing time
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).
DESeq2 experimental design and interpretation
Demos of extracting and interpreting DESeq2 results. Importance of properly setting reference levels for factors.