scripts/PIPELINE_INDEX.md

Research pipeline index

The public source subset is grouped by purpose; chronological numbers preserve the frozen execution lineage. Exact scripts containing donor/cell identifiers are withheld and described in protocols/REDACTED_FROZEN_STAGES.md.

Environment and upstream inventory

• 01_system_preflight.py
• 03_inventory_manifest.py
• 04_c2s_smoke_test.py

Metadata and taxonomy

• 05_audit_small_metadata.py
• 06_preview_cell_metadata.py
• 07_download_full_metadata_and_taxonomy.py
• 08_build_mtg_annotated_metadata.py
• 09_audit_mtg_taxonomy_and_qc.py

Frozen donor design and MTG matrix

• 10_generate_donor_split_candidates.py
• 11_freeze_donor_split.py
• 12_download_mtg_raw_matrix.py
• 13_inspect_mtg_raw_matrix_v3.py
• 14_build_primary_cell_index.py
• 15_create_sampling_manifests.py

Ranked-gene and C2S representation

• 18_rebuild_ranked_gene_records_c2s_aligned.py
• 19_full_development_token_audit.py
• 20_create_c2s_base_pilot_manifest.py
• 21_run_c2s_base_model_pilot.py
• 22_compare_c2s_base_pilots.py
• 23_create_score_vector_manifests.py
• 24_extract_c2s_exact_score_vectors.py
• 25_fit_c2s_score_vector_classifier.py
• 26_audit_score_vector_signal.py
• 27_extract_c2s_frozen_embeddings_v2.py
• 28_fit_c2s_embedding_probe.py
• 29_audit_embedding_probe_signal.py

Classical and raw-expression baselines

• 30_build_classical_rank_features.py
• 31_fit_classical_rank_baselines.py
• 32_compare_development_baselines.py
• 33_build_raw_hvg_features.py
• 34_fit_raw_hvg_baseline.py
• 35_create_canonical_marker_masked_manifests.py
• 36_fit_canonical_marker_masked_baselines.py
• 37_summarize_in_region_development.py

Assay transfer

• 38_build_multiome_transfer_manifests.py
• 39_build_multiome_ranked_gene_records.py
• 40_build_multiome_transfer_features.py
• 41_evaluate_multiome_transfer.py

Region transfer

• 42_audit_region_transfer_candidates.py
• 43_download_mec_raw_matrix.py
• 44_inspect_and_build_mec_transfer_manifests.py
• 45_build_mec_ranked_gene_records_v2.py
• 46_build_mec_transfer_features.py
• 47_evaluate_mec_transfer.py

Donor-level AD severity

• 48_audit_ad_progression_feasibility.py
• 50_build_ad_severity_donor_features.py
• 51_fit_ad_severity_training_baselines_v1_1.py
• 52_evaluate_ad_severity_validation.py

Deliberately withheld exact sources

• frozen MEC one-cell compatibility exclusion wrapper: contains an exact cell and donor identifier;
• frozen AD feature-cohort bias-audit script: contains exact donor identifiers;
• frozen donor split configuration: contains donor-level assignments;
• all prediction, embedding, matrix, and joblib artifacts.