These are real project workflows retained for provenance, practical context, and worked examples. They may contain project-specific paths, identifiers, labels, assumptions, or external inputs and are not guaranteed to run from a clean clone.
The reusable generalized versions are under ../templates/.
Current groups include:
single_cell/map/: MAP RNA/ATAC and downstream analyses;single_cell/gse171145.qmd: an external single-cell cohort workflow;bulk_rna/mgi_organoids/: organoid QC, GSEA, and Hallmark scoring;biomarker_ml/trento/: TRENTO model and reporting notebooks;multiomics/tcga_mofa/: TCGA/MOFA workflows;multiomics/cptac_luad/: CPTAC-LUAD scoring.