Untargeted metabolomics pipeline, release p1.1
phalaena:pipeline:PA-PL-metabolomics
Untargeted LC-MS metabolomics: spectral preprocessing, feature finding, a cross-sample feature matrix, plots, and a canonical summary/summary.json. We centroid each spectrum, group isotope patterns into chromatographic features, align those features across samples into a sample-by-feature matrix, and emit the matrix as the pipeline contract. There is no compound-identification step inside the pipeline (no MS2 library matching, no SIRIUS, no GNPS); the feature matrix is the contract the assistant reads. Pipeline ID metabolomics. Source: phalaena_backend/pipelines/4_metabolomics/. API entry: phalaena_api/app/pipelines/metabolomics.py.
- kind
- pipeline
- assay
- untargeted LC-MS
- status
- reviewed
- github:phalaena-automata/monorepo/phalaena_backend/pipelines/4_metabolomics
View Untargeted metabolomics pipeline, release p1.1 on the Phalaena Wiki