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epigen / RnBeads

Git working Repo synced to the Bioconductor: http://bioconductor.org/packages/devel/bioc/html/RnBeads.html
https://rnbeads.org/
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Support for the Illumina Mouse Array #14

Closed schmic05 closed 4 months ago

schmic05 commented 3 years ago

Supporting the mouse array was requested by a number of users and will be a great addition to the package. Here is the info for the array (https://emea.illumina.com/products/by-type/microarray-kits/infinium-mouse-methylation.html) and the associated manifest (https://emea.support.illumina.com/downloads/infinium-mouse-methylation-manifest-file-bpm.html).

lutsik commented 3 years ago

Hi guys.

I already have a branch where the import of the mouse array is essentially implemented. Maxi (a PhD student over here) has managed to build an annotation package.

Should I first commit the branch so we can look at it together and discuss?

lutsik commented 3 years ago

see feature/MouseMethylationBeadChip

schmic05 commented 3 years ago

Hi Pavlo,

That's great news. Yes, let's have a look at the branch together and maybe discuss it afterwards. Thanks for developing this and greetings to Maxi.

lutsik commented 3 years ago

Sure, will do ))

acherman commented 3 years ago

Hi All,

What's the status of the support for the mouse array? Should I grab that branch and give it a go?

Thanks for the tools!

lutsik commented 3 years ago

The branch alone will not help, since you also need an updated RnBeads.mm10. The latter is still in the making, hang on a little longer...

RinconFer commented 5 months ago

Hi thanks for the fantastic package,

I am trying to use it to analyze a mouse dataset, however I have been unable to install the development version because it is asking for the R version 4.4 and I can't install that without really breaking all my other pipelines to analyze other type of data. Is there a way to use the package in mouse data without being force to install the development version of R?

schmic05 commented 5 months ago

Hi @RinconFer

As far as I know, this will unfortunately not be possible. However, I would suggest that you look into (bio)conda (https://bioconda.github.io/), which makes it easy to have multiple different R installations in parallel.

Hope that helps,

Michael