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.