SynPDClassify

Not a new plugin — a pipeline recipe that composes the Syn* protein-level plugins with existing PluMA classifier and plotting plugins to produce a case/control PD discrimination workflow.

Research tool, not a clinical diagnostic.

Pipeline

[proteomics TSV]         [ELISA CSV]
      |                        |
      v                        v
SynProteinFilter (total)   SynAssayQuantify
SynProteinFilter (pS129)
      |
      v
SynPhosphoRatio
      |
      v
[feature matrix]
      |
      +------> DESeq / Limma  (case-vs-control stats)
      +------> LogReg / RandomForest / SVM  (classifier)
      +------> PlotROC  (AUROC figure)

What this gives a Parkinson's researcher

• Per-sample biomarker vector: (total_alpha_syn, ps129_ratio, agg_index, assay_conc)
• Cohort-level discrimination: ROC/AUC, significance tests
• Stratification inputs: drop into DimReduc/* plugins (PCA, UMAP) for PD vs DLB vs MSA vs control clustering, or join on clinical covariates (UPDRS, MDS-UPDRS, MMSE) in downstream sample-keyed plugins.

Example config.txt

See example/config.txt. The pipeline assumes you have already placed fixtures from the upstream plugins' example/ directories — or supplied your own data in the same formats.