I agree that there is the need to be able to do the comparisons systematically, and have a good dataset to perform them.
Also, I think these methods papers provide comparisons that do not always make sense. Perhaps they want to illustrate something (e.g. cuffdiff2 better than doing RSEM/IsoEM/etc + EdgeR/DESeq ).
But there are other methods that have been explicitly developed to calculate the differential expression of isoforms between two conditions (at least they claim so in their papers 8-) ). I've been able to gather these (including Cuffdiff2):
BASIS
Alexa-Seq
FDM
MISO
rDiff
Cuffdiff2
DSGSeq
Some already mentioned here. So wouldn't it make sense to perform comparisons between methods alike rather than an all against all?
E.
Also, I think these methods papers provide comparisons that do not always make sense. Perhaps they want to illustrate something (e.g. cuffdiff2 better than doing RSEM/IsoEM/etc + EdgeR/DESeq ).
But there are other methods that have been explicitly developed to calculate the differential expression of isoforms between two conditions (at least they claim so in their papers 8-) ). I've been able to gather these (including Cuffdiff2):
BASIS
Alexa-Seq
FDM
MISO
rDiff
Cuffdiff2
DSGSeq
Some already mentioned here. So wouldn't it make sense to perform comparisons between methods alike rather than an all against all?
E.
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