EuracBiomedicalResearch / end-to-end-untargeted-metabolomics

A simple end-to-end untargeted metabolomics analysis workflow
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End-to-end-untargeted-metabolomics

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:

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:

-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!