KissDE and batch effect
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1
Entering edit mode
8 weeks ago

Hello,

due to "reasons", I have a somewhat important batch effect in a cohort, that is impacting quite negatively my splicing analysis. Is there any way that this could be "dealt with" in KissDE (or with another way ?), like it can be done with DESeq2 (modeling the effect by including it into the design formula : ~ batch + condition) ?

By the way, the new --type1-only parameter in KisSplice 2.6.2 is quite a nice addition, thanks!

Best,

David.

kissDE kissplice • 301 views
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2
Entering edit mode
26 days ago

Hello,

I do not think this is yet possible with kissDE, even though it could be a quick, easy and nice addition to the package! Maybe in the near future...?

Oh, you noticed that option? Cool! Indeed, it can save a lot of time for people only interested in AS events (even though some AS events could be found in the type 4...).

Have you noticed the Shiny Interface that comes with the lastest version of kissDE? We hope that it can help users to quickly navigate and identify interesting entries in kissDE results...

Best, Audric

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0
Entering edit mode

Hello,

then I will wait for a future update !

Although I noticed the new rds file with writeOutputKissDE, I didn't even know there was a Shiny interface. And wow, it looks quite handy, really cool addition, thanks !

Best, David

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