Untargeted pipeline demo (WIP) #298
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* Add skeleton untargeted pipeline directory with plan * fix flake8 errors in generate chemicals script * Add lint/test guidelines and minimal untargeted test * Implement dataset setup script * Add mzML generation step * Tune chromatogram width * Add ground truth table generation * Add MGF export for simulated chemicals * docs: mark simulation step complete
* Add metric reporting helper to pipeline * Add linear column RT noise option * Add RT drift models and use in demo pipeline * Refactor drift models into main package * Clean up drift and demo scripts
* Refactor output handling and add get_peak_data * Refactor pipeline into classes
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PR to add demo using vimms to generate synthetic data so we can test the performance of a typical untargeted data processing pipeline in LC/MS metabolomics.
So we generate chemicals in various experimental setup, write their mzml files + corresponding ground truth. The mzml files are then passed into a pipeline that tries to infer back chemical identities from spectral data. Since it's synthetic data, we can easily evaluate pipeline performance for all these steps:
Still work in progress, do not merge yet!!