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EuracBiomedicalResearch / end-to-end-untargeted-metabolomics

A simple end-to-end untargeted metabolomics analysis workflow
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Pre-rendered document? #38

Open TuomasBorman opened 1 day ago

TuomasBorman commented 1 day ago

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 commented 5 hours ago

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 commented 4 hours ago

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 :)