scripts/pan_skin
canonical end-to-end pipeline for the pan-skin corpus. steps are numbered in the
order they need to run. everything writes into data/corpus/pan_skin/,
checkpoints/pan_skin/, and figures/.
| step | script | what it does |
|---|---|---|
| 01-03 | 01_download_tier_a.sh .. 03_download_tier_c.sh |
fetch tier A/B/C raw h5ads + counts |
| 06 | 06_build_per_dataset_h5ads.py |
per-dataset QC + h5ad build |
| 07 | 07_build_shared_hvgs_and_pca.py |
shared HVGs + PCA basis over the union |
| 08 | 08_assign_labels.py (+ 08b_curated_label_override.py) |
marker-scored labels, Sulic overrides |
| 10 | 10_build_corpus.py |
merged harmonized corpus.h5ad |
| 20 | 20_train_panda.py |
PANDA-MLP with hybrid sampling |
| 30 | 30_zero_shot_aldrich.py |
inference on Aldrich / Dingwall (held-out target) |
| 40 | 40_heldout_5fold_cv.py |
5-fold CV, PANDA retrained from scratch per fold |
run_all.sh chains these in order. marker panels: known_skin_tfs.yaml; ontology
map: ontology_map.yaml.