File size: 3,178 Bytes
6546c58 c589708 092211f 6546c58 092211f c589708 092211f c589708 092211f c589708 092211f c589708 092211f c589708 092211f c589708 092211f c589708 092211f c589708 092211f c589708 092211f c589708 092211f | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 | ---
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
```
|