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Add DeSeq2 support (Read 1099 times)
Aug 6th, 2019 at 4:28pm

Mike Shelk   Offline
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Hi!

Currently UGENE uses cuffdiff for differential expression analysis. Cuffdiff is outdated and produces more false positives than many other tools. I think many people will be glad if you add a more modern tool for the differential expression analysis, for example DeSeq2. A comparison can be found in the paper "How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?" (2016).
 
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Reply #1 - Aug 12th, 2019 at 1:41pm

Olga Golosova   Offline
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Hi Mike!

Thank you for the feedback!

We plan to integrate DeSeq2, however for now we can't specify the exact deadlines when this will be done.
 
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Reply #2 - Dec 28th, 2020 at 11:36pm

alfredlan   Offline
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Great! DeSeq2 is a really helpful tool. It would improve the performance of UGENE. That was a valuable suggestion.
 
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Reply #3 - Feb 10th, 2021 at 10:43pm

Brielle Luna   Offline
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What a great suggestion!
 
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Reply #4 - Feb 17th, 2021 at 10:47pm

Kenny   Offline
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Thanks for the information!
 
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