For example, Dioxin Response Elements, Estrogen Response Elements, etc. Please provide any specific statistical tests or online tools to perform analysis of the response elements.
If in R&D environemnt develop your own script in R/Rstudio (free to install; supported by both Linux/Windows). For validated environment switch to SAS (definitively not free...;-) ).
Both provide all functionnalities required to perform stats.
You will find hundreds of R scripts on the WZEB (see also CRAN for ready to use packages).
There are an awkward big number of analyses you can make from the results of RNA-seq, depending on your biological question. Try to define enriched GO terms of your genes, or KEGG pathways to number a few. I am not sure if this is what you want. But if is, one very handy tool is Bioconductor package clusterProfiler ( https://www.bioconductor.org/packages/release/bioc/html/clusterProfiler.html ).
I hope it helps. Cheers.
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