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

Sorry I'm not familiar with this type of data. DESeq2 is fairly broadly useful for comparing across many features when you have independent samples in different groups. Usually the place where it breaks down is when there are not clear groups of features that had little or no change, e.g. no "housekeeping" features.