| # Data and partitions |
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| The full adapters read count matrices from scPerturb record 10044268. Norman contains K562 CRISPR activation experiments with single-gene and two-gene conditions. The Replogle adapter selects the K562 essential-gene interference screen. The source files are approximately 0.70 GB and 1.55 GB, respectively. |
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| Required input: an AnnData `.h5ad` file with unique cell and feature IDs, a nonnegative count matrix, and `obs.perturbation`. The control label is `control`; underscore-separated gene names denote combinations. Optional context columns default to `gemgroup` and `celltype`; they can be set explicitly with CLI flags. For Replogle, pass `--batch-col batch --celltype-col cell_line` to preserve the source context columns. Missing context columns produce one documented dataset-wide context. A requested batch-matching operation fails if no allowed controls match a response cell. |
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| The cache contains normalized sparse expression, PCA coordinates, basis and mean, feature order, cell metadata, and checksums. PCA is an affine reconstruction of retained components and is lossy. Metadata-only gene identities may include held-out genes. Their learned embedding rows receive no response supervision when those genes are absent from training. |
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| | Partition regime | Unit assigned to a partition | |
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| | `cell` | Cells within every condition, 70/15/15 | |
| | `perturbation` | Complete intervention labels, approximately 70/10/20 | |
| | `combination` | Two-gene conditions, approximately 70/10/20; singles remain in training | |
| | `gene` | Gene identities; every containing intervention follows the held-out gene | |
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| Controls are partitioned independently. Approximately 10% of each condition's cells are reserved as `reference` outcomes before fitting expression features. Reference cells do not fit the model, determine validation selection, or form target queries. They are used to measure the response quality of a nominated action. The independent experimental unit for summary intervals is a condition. Separate cells from one screen do not establish cross-study biological replication. |
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| The included fixture has 920 measured Norman cells, 20 perturbed conditions, 120 controls, and 33,694 source features. The selection uses seed 17. `provenance.json` records the source checksum and retained cell IDs. The example selects approximately 200 variable genes; the dispersion threshold can retain ties, so the tested cache retained 201 features and 10 principal components. |
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| For cross-study evaluation, freeze the source transformation and explicitly align genes before projection. No cross-cell-type or cross-study transfer result is reported in this release. |
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