Hi,
In the genome we are working, we've established the co-occurrence (presence) of transposons and a type of genes along the genome (t-test given a window size).
I'm wondering if this could be made with RNAseq profiles; that the transcription of one gene is also correlated with the transcription on its neighbours, and if somehow the analysis can be done using RNA count levels.
If you have any suggestion on how would you do it or any kind of feedback, I will appreciate it. Thanks
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