DE Analysis between genotypes

fanyue322 / TDEseq

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DE Analysis between genotypes #3

Open yashuap opened 3 months ago

yashuap commented 3 months ago

We have a dataset consisting of 4 different genotypes. While we are able to use this package to identify DE genes and their patterns for each genotype individually, we were wondering if there is a way to compare it between genotypes to determine what is DE between different genotypes beyond just manually comparing them (i.e. comparing the "SignificantDE," "pattern," and "ChangePoint" columns between genotypes).

fanyue322 commented 3 months ago

Hi yashuap,

Currently, TDEseq can only handle data that come from identical conditions. Perhaps you can try tradeSeq or ImpulseDE2; both of them can detect DE genes between two different conditions.

Best