TOMOseq DEG analysis

Question

[moutazhatem.mh]

Dear All,

Thank you for reading my question.

I am trying to analyze a TOMOseq data set which basically a bulk RNAseq of consecutive section of a a tissue. I am using "tomoda" R package for this analysis.

I have some few questions:

1. Is their any other packages I can use for the analysis?
2. Would it be possible to use DESeq2 for the analysis? If yes, how can I make a design to be able to compare every section or a specific section or multiple sections to the rest of the sections?

Thank you for the help