Hello everyone,

I am trying to perform super enhancer analysis using timepoint data. I used the ROSE tool to find super enhancers, but I cannot figure out how to proceed with the downstream analysis.

My initial idea was to continue with the DESeq2 package and use the LRT test to identify significant super enhancers, then integrate those results with transcriptome data. However, I am still not sure if this is the best approach or how exactly to perform this integration.

I also cannot use DiffBind package because I only have two replicates per timepoint, which prevents proper contrast generation.

I would appreciate any suggestions on the best workflow for analyzing dynamic super enhancers across timepoints and integrating them with transcriptome results.

Thank you.