| # External Reference Data |
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| This folder is the clean, reusable external-data surface for Z-Screen benchmarking. |
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| Start with: |
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| - `catalog/processing_provenance.md` for what was copied, converted, and not recomputed. |
| - `catalog/external_reference_dataset_catalog.csv` for dataset-level entry points. |
| - `catalog/external_reference_file_manifest.csv` for file-level hashes and legacy source aliases. |
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| Most experiments should use the Parquet tables under: |
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| - `crispr_perturbation_atlases/` for Replogle, Norman, and selected THP1 scPerturb CRISPR comparisons. |
| - `compound_atlases/lincs_l1000/processed/` for LINCS L1000 compound signature comparisons. |
| - `compound_atlases/tahoe_100m/metadata/` for Tahoe metadata-only overlap checks. |
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| `benchmark_outputs/` contains the prior LINCS versus Z-Screen overlap/correlation outputs from the legacy benchmark bundle. Treat those as historical benchmark outputs, not as primary external atlas inputs. |
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| Raw external H5AD and LINCS GCTX matrices are not bundled here. The processed rank-signature tables and provenance scripts are bundled so downstream experiments do not need to rebuild them for routine comparisons. |
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