| # 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. |
|
|
