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Question: Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
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gravatar for kristoffer.vittingseerup
9 months ago by
European Union

I have just read the DRIMSeq article ( https://f1000research.com/articles/5-1356/v2 ) and tried the Bioconductor R package ( https://bioconductor.org/packages/release/bioc/html/DRIMSeq.html ) and I think it has great potential.

I was simply wondering whether it was possible to get an estimate for the differential usage of each isoform instead of each gene? This would make downstream analysis a lot easier since one would know exactly which isoforms were differentially used instead of just knowing that some (of the potentially many) isoforms within this gene were changing.

It would basically correspond to getting a p-value for each isoform proportion/fraction.

 

Kindest regards

Kristoffer

ADD COMMENTlink modified 9 months ago by gosia.nowicka10 • written 9 months ago by kristoffer.vittingseerup20
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gravatar for gosia.nowicka
9 months ago by
gosia.nowicka10 wrote:

Dear Kristoffer, 

I am glad you find DRIMSeq useful. 

I have been working on implementing the isoform-level analysis which are based on the beta-binomial distribution. 

Additionally, there will be a full regression framework available for gene-level and feature-level analysis allowing for modeling more complicated designs. 

All these features will be available with the new Bioconductor release 3.5. 

Currently, the development version of these implementations is available on DRIMSeq github https://github.com/markrobinsonuzh/DRIMSeq, but I suggest to wait until they are pushed to the devel version of Bioconductor since they are updated very intensively.

Kind regards,

Malgorzata

ADD COMMENTlink written 9 months ago by gosia.nowicka10

That sounds extremely usefull - both the feature level test but also the complex designs! Looking forward to try it!

ADD REPLYlink written 7 months ago by kristoffer.vittingseerup20
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