| --- |
| pretty_name: CellClip public normalized perturbation single-cell release |
| license: other |
| task_categories: |
| - feature-extraction |
| tags: |
| - single-cell |
| - transcriptomics |
| - perturb-seq |
| - h5ad |
| - human |
| --- |
| |
| # CellClip public normalized perturbation single-cell release |
|
|
| This public repository contains the source-cleared, human, cell-level portion |
| of CellClip Stage 1: **254 H5AD files**, **12,718,270 cells**, and |
| **260,859,318,437 payload bytes**. These are processed derivatives rather than |
| the original raw download archives. |
|
|
| | Source partition | Units | Cells | Reference cells | Effect cells | |
| |---|---:|---:|---:|---:| |
| | scPerturb (23 genepert + 229 chempert) | 252 | 4,774,802 | 397,528 | 4,377,274 | |
| | XCell / X-Atlas Orion (genepert) | 2 | 7,943,468 | 384,615 | 7,558,853 | |
| | **Total** | **254** | **12,718,270** | **782,143** | **11,936,127** | |
|
|
| The repository intentionally excludes all PerturBase-derived files. Those |
| files have no verified package-level redistribution permission and are held in |
| a separate private repository. The OT-center release is also separate. |
|
|
| ## Data contract |
|
|
| - `X` is per-cell `normalize_total(target_sum=1e4)` followed by natural |
| `log1p`. |
| - Confirmed raw UMI counts are retained in `layers["counts"]`. |
| - `obs["is_reference"]` is the authoritative reference mask; do not infer |
| controls from filenames or loose regular expressions. |
| - Gene perturbation targets are standardized in `target_gene_symbol`; consult |
| `target_gene_symbol_status` before foundation-model vocabulary filtering. |
| - `obsm["X_scVI"]` is a 30-dimensional representation independently trained |
| within each H5AD. It is not a shared coordinate system across files. |
| - Machine-readable unit, batch, source, transformation, license, and SHA-256 |
| metadata are under `manifest/`. |
|
|
| The path spelling `scPeturb/` is retained for release compatibility, while the |
| machine-readable source value is `scPerturb`. |
|
|
| ## License boundary |
|
|
| There is no single permissive license for this repository, so the dataset card |
| uses `license: other`: |
|
|
| - `scPeturb/` is adapted from scPerturb v1.4 under **CC BY 4.0**. Reuse must |
| attribute scPerturb and the original studies, link the license, and identify |
| CellClip's transformations. |
| - `xcell/` is adapted from Xaira Therapeutics X-Atlas Orion under |
| **CC BY-NC-SA 4.0**. This partition is noncommercial, requires attribution |
| and change indication, and must remain ShareAlike. See `xcell/LICENSE.md`. |
|
|
| Keeping these path partitions together is aggregation, not a relicensing of |
| either source. Users must apply the terms of the partition they download. |
|
|
| ## Integrity and selective download |
|
|
| `manifest/UPLOAD_MANIFEST.tsv` contains exactly the 254 H5AD objects present in |
| this repository. `manifest/RELEASE_FILES.tsv` and `SHA256SUMS` are generated |
| specifically for this repository and contain no PerturBase or OT-center paths. |
|
|
| The two XCell files are very large. Prefer selective downloads and backed or |
| sliced reads instead of cloning the full repository: |
|
|
| ```bash |
| hf download cfy2yue/perturbseq_normalized \ |
| scPeturb/model_ready/genepert/<training-unit>.h5ad \ |
| --repo-type dataset --local-dir perturbseq_normalized |
| ``` |
|
|
|
|
