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Datasets:
cfy2yue
/
perturbseq_normalized

Tasks:
Feature Extraction
Tags:
single-cell
transcriptomics
perturb-seq
h5ad
human
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Dataset card Files
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Upload scPerturb normalized payload

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scPeturb/README.md ADDED
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1
+ # scPerturb-derived model-ready H5AD
2
+
3
+ This directory contains 252 human cell-level derivatives prepared from the
4
+ scPerturb collection: 23 gene-perturbation units and 229 chemical-perturbation
5
+ units. It does not contain the upstream raw downloads.
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+
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+ | modality | units | cells | reference | effect |
8
+ | --- | ---: | ---: | ---: | ---: |
9
+ | genepert | 23 | 3,468,800 | 218,422 | 3,250,378 |
10
+ | chempert | 229 | 1,306,002 | 179,106 | 1,126,896 |
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+
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+ For every file, `X` is per-cell CP10K natural `log1p`, confirmed raw UMI counts
13
+ are in `layers["counts"]`, and the independently trained 30-dimensional scVI
14
+ representation is in `obsm["X_scVI"]`. Control/reference selection must use
15
+ `obs["is_reference"]`; vehicle/DMSO must not be reinterpreted as untreated or
16
+ time zero.
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+
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+ The on-disk directory name `scPeturb` is a retained historical spelling. The
19
+ machine-readable source label and center paths use `scPerturb`; paths are
20
+ case-sensitive. Always obtain paths from `../manifest/TRAINING_UNITS.tsv`.
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+
22
+ These are processed/model-ready derivatives, not raw source files. Read
23
+ `../README.en.md`, `../DATA_DICTIONARY.md`, and `../USAGE.md` before use. The
24
+ source release, original-study citations, licenses, and redistribution status
25
+ must be taken from the Stage 1 source-provenance table; do not infer a data
26
+ license from the scPerturb software repository.
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+
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+ The audited redistribution basis for these files is the scPerturb v1.4 dataset
29
+ record (`10.5281/zenodo.13350497`), which applies CC BY 4.0. Public release must
30
+ attribute scPerturb and each original study, link the license, and identify the
31
+ CellClip modifications described in `../PROCESSING.md`.
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