A simple end-to-end untargeted metabolomics analysis workflow.
IMPORTANT: we are currently working on data availability, it is (hopefully) coming soon.
Some preparation steps:
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Please ensure you have the latest version of R installed locally. You can find about it here: url
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Packages: you can copy/paste the code down here to install the bioconductor packages needed to run the analysis. If at any point when running the code you get an error message that a function cannot be found tell me and I will help. We also advise to chack for update as often as possible so you can properly enjoy the latest development in LC-MS/MS analysis.
BiocManager::install("rformassspectrometry/Spectra")
BiocManager::install("sneumann/xcms")
BiocManager::install("RforMassSpectrometry/ProtGenerics")
BiocManager::install("RforMassSpectrometry/MsCoreUtils")
BiocManager::install("RforMassSpectrometry/Spectra")
BiocManager::install("RforMassSpectrometry/MSnbase")
BiocManager::install("RforMassSpectrometry/MetaboCoreUtils")
BiocManager::install("RforMassSpectrometry/CompoundDb")
BiocManager::install("RforMassSpectrometry/MetaboAnnotation")
BiocManager::install("RforMassSpectrometry/MsExperiment")
BiocManager::install("RforMassSpectrometry/MsBackendSql") # no need for now but maybe later
BiocManager::install("RforMassSpectrometry/SummarizedExperiment")
The other packages are part of CRAN so should be easy to install.
For co-auhtors:
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Don't forget to regularly check if the main branch was updated and merge it with your own branch as to not get out of sync with the main branch.
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I would advise to do your review by chunks such as: preprocessing, normalization/filtering, differential abundance analysis, annotation. This way we avoid super big pull request.
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Don't hesitate to make changes, we need your input ! We can discuss when you do the pull request.
-We will publish in the journal F1000 you can check this tosee the format we are aiming for: url
Don't hesitate to contact me or johannes if you have technical problems
Good reading and thanks again!