| # scPerturb-derived model-ready H5AD |
|
|
| This directory contains 252 human cell-level derivatives prepared from the |
| scPerturb collection: 23 gene-perturbation units and 229 chemical-perturbation |
| units. It does not contain the upstream raw downloads. |
|
|
| | modality | units | cells | reference | effect | |
| | --- | ---: | ---: | ---: | ---: | |
| | genepert | 23 | 3,468,800 | 218,422 | 3,250,378 | |
| | chempert | 229 | 1,306,002 | 179,106 | 1,126,896 | |
|
|
| For every file, `X` is per-cell CP10K natural `log1p`, confirmed raw UMI counts |
| are in `layers["counts"]`, and the independently trained 30-dimensional scVI |
| representation is in `obsm["X_scVI"]`. Control/reference selection must use |
| `obs["is_reference"]`; vehicle/DMSO must not be reinterpreted as untreated or |
| time zero. |
|
|
| The on-disk directory name `scPeturb` is a retained historical spelling. The |
| machine-readable source label and center paths use `scPerturb`; paths are |
| case-sensitive. Always obtain paths from `../manifest/TRAINING_UNITS.tsv`. |
|
|
| These are processed/model-ready derivatives, not raw source files. Read |
| `../README.en.md`, `../DATA_DICTIONARY.md`, and `../USAGE.md` before use. The |
| source release, original-study citations, licenses, and redistribution status |
| must be taken from the Stage 1 source-provenance table; do not infer a data |
| license from the scPerturb software repository. |
|
|
| The audited redistribution basis for these files is the scPerturb v1.4 dataset |
| record (`10.5281/zenodo.13350497`), which applies CC BY 4.0. Public release must |
| attribute scPerturb and each original study, link the license, and identify the |
| CellClip modifications described in `../PROCESSING.md`. |
|
|
