[Tool Request]: geNorm / NormFinder

[TWV-GIT]

I would like to request a galaxy tool based on either the geNorm or NormFinder (preferably geNorm) algorithms which serve to determine the most stable housekeeping genes for qPCR analysis. Both are publicly available and much requested in my lab as well as elsewhere.

For geNorm, there is an excel script: https://tinyurl.com/geNorm For NormFinder, there is also an excel script: https://moma.dk/files/NormFinder_0953.xla As well as an R script: https://moma.dk/files/r.NormOldStab5.txt

I look forward to your responses. Greetings, TWV.

[bgruening]

Looping in @pavanvidem, our qPCR expert.

There is a standard RDML (http://www.rdml.org/software.php) st by some consortium to follow MIQE 
guidelines. But people are working with CSV and excels. There are some qPCR machines which directly
 output rdml format. There are some tools out there which can work with RDML. If we encourage people to
 use this, there will be no excel copying.
But first, we need to contact the RDML people about how well established this format and if it still maintained 
or need any maintenance.

[TWV-GIT]

There is already an R package that can do what I request here and more: https://www.rdocumentation.org/packages/NormqPCR/versions/1.18.0

I think the "selectHKs" function is the most interesting. I wouldn't know how to go about integrating that into Galaxy though. I am but a mere biologist!

[TWV-GIT]

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[TWV-GIT]

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[mblue9]

@TWVKUL I might be able to help with this when I can get time, but first there needs to be a conda package for NormqPCR as that doesn't exist yet. (P.S. I was once a 'mere biologist' doing real-time qPCR too 😄)

[bgruening]

I will add this to the GCC2019 project board! Let's see if someone picks it up.

[TWV-GIT]

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[TWV-GIT]

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