Xijin Ge

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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
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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.