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federicomarini / GeneTonic

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
https://federicomarini.github.io/GeneTonic
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GeneTonic with EdgeR #26

Closed lucolotto closed 2 years ago

lucolotto commented 2 years ago

Hi Federico, First of all, thanks for the great package. It is a very useful and interesting tool. Really a great job! Thanks

I was wondering if you could adopt your library to accomodate also people that use edgeR for DE calling. I was thinking maybe at some sort of shake function that would take a DGEList object from edgeR and create a "fake" DEseqResult object, with just the minimal info needed for GeneTonic to work. Would that be possible?

Thanks a lot Luca

federicomarini commented 2 years ago

Hi Luca,

Would the section in the Supplements of the recently published paper be something for your case?

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04461-5

See Additional file 3 ->

image

The function to convert between formats should already be a part of the DEformats package

lucolotto commented 2 years ago

That is exactly what I needed, thanks a lot Federico! Much appreciated. I also looked at your other projects, pretty impressive work. I will try also your pcaExplorer and ideal libraries

federicomarini commented 2 years ago

Perfect, glad it could help. I could/should link to that content in the vignette of the package - will do that in the Bioc/GitHub devel branch for now 😉

Can this one be safely closed otherwise? Federico

p.s. Thanks for the kind words - if you are into single cell analysis, have a look at the iSEE package as well 🎉 (https://github.com/iSEE/iSEE)

lucolotto commented 2 years ago

Thanks! yes, for me you can safely close this. I will have a look at iSEE as well for the sake of curiosity (I am not doing single cell sequencing at the moment, but in the future who knows!?!?).

Happy 2022! Luca