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Datasets:
cfy2yue
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perturbseq_normalized

Tasks:
Feature Extraction
Tags:
single-cell
transcriptomics
perturb-seq
h5ad
human
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perturbseq_normalized / README.md
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metadata 
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:

hf download cfy2yue/perturbseq_normalized \
  scPeturb/model_ready/genepert/<training-unit>.h5ad \
  --repo-type dataset --local-dir perturbseq_normalized