Update workflow to incorporate MALDIquantForeign and MALDIquant

LizzyParkerPannell / Untargeted_metabolomics_workflow

Collaborative workflow for untargeted metabolomics data processing and analysis using open-source tools. https://doi.org/10.3390/metabo13040463

https://untargeted-metabolomics-workflow.netlify.app/

GNU Affero General Public License v3.0

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Update workflow to incorporate MALDIquantForeign and MALDIquant #23

Open LizzyParkerPannell opened 1 year ago

LizzyParkerPannell commented 1 year ago

Now that we've sorted the file conversion parameters to get MALDIquant to work in R, can adapt the workflow with MassUp being optional (still good for QC)

[ ] update R codes for step 04_data-preprocessing (MALDI and DIMS)
[ ] update guide/ documentation to explain the options
[ ] link directly to MALDIquantForeign and MALDIquant vignettes as these are very good

LizzyParkerPannell commented 1 year ago

@Jkellaway is this what you were talking about yesterday? I've got it working on somebody else's data now so hoping to share notes soon