Pre-rendered document?

[TuomasBorman]

Thank you for the excellent workflow! I'm currently exploring it to familiarize myself with the field, and it seems like a perfect fit. However, the Rmd file is not directly reproducible at the moment, as the "data" directory is missing the metabolite files. Would it be possible to either include the necessary data or provide a pre-rendered HTML/PDF version of the workflow?

Best regards,
Tuomas

[jorainer]

We're currently working on a way to directly fetch the data from the MetaboLights repository. Then the whole workflow would be completely reproducible. @philouail , how long do you think it will take to get that into the workflow?

[philouail]

Hello @TuomasBorman I am still working on moving the workflow to its final place.
The fetching to MetaboLights works now and is integrated in the workflow you can find in this repository:
https://github.com/rformassspectrometry/metabonaut
Please check the README,md for the known issues and the manual installation that you might need to do, as I said it is still a work in progress. I am hoping to fix all the bugs and have it deployed in a website this week/next week. However, it should be reproducible now.

Don't hesitate if you have more questions :)

[TuomasBorman]

Thanks! I will check it as soon as time allows. Moreover, it was nice that I noticed that you have methods for fetching the data from MetaboLights. We have develop HoloFoodR package that fetches data from HoloFood database. The database does include only part of the data; for certain data types it just points to other database. One of these is MetaboLights.

In spring, I did not find existing methods for fetching the data from MetaboLights, and ended up developing simple method for that. I realized that your method is better if user wants to fetch the spectra files directly to MsExperiment.