README.md

metadata

language:
  - en
  - zh
license: other
task_categories:
  - feature-extraction
tags:
  - single-cell
  - transcriptomics
  - perturbation
  - drug-response
size_categories:
  - 10K<n<100K
pretty_name: Curated Single-Cell Drug Perturbation Benchmarks

Curated Single-Cell Drug Perturbation Benchmarks

This release contains 20 single-cell drug-perturbation benchmarks linked to 20 distinct papers. Each benchmark includes one control expression matrix, one treated ground-truth matrix, and a JSON test specification. The selection prioritizes broad target-gene panels and agreement between the encoded target directions and the main conclusions of the source paper.

Release status and license

The benchmark metadata is prepared for release, but redistribution rights for the derived H5AD files must be confirmed from the original studies before making the repository public. license: other is intentionally conservative and does not grant rights beyond those of the source datasets. Users remain responsible for complying with the original study terms and citing the corresponding paper.

Files

README.md
benchmarks.csv
release_manifest.csv
release_audit.json
data/
  <benchmark_id>/
    control.h5ad
    ground_truth.h5ad
    test_case.json

The 60 core data files total 30.4 GiB. release_manifest.csv records the exact byte size and SHA256 digest of each file. Local source paths are excluded from the public manifest.

Benchmarks

Rank	Benchmark	PMID	Perturbation	Tissue	Targets	Direction agreement
1	38937474_01	38937474	osimertinib	Lung	34	32/34 (94.1%)
2	38895265_01	38895265	Paclitaxel	Breast	18	18/18 (100.0%)
3	34591417_01	34591417	vemurafenib	Skin	14	14/14 (100.0%)
4	40766395_01	40766395	Brefeldin A	Liver	14	14/14 (100.0%)
5	37086265_01	37086265	etoposide	Lung	18	16/18 (88.9%)
6	33712615_01	33712615	erlotinib	Lung	19	15/19 (78.9%)
7	32846134_01	32846134	5-fluorouracil	Colon	9	9/9 (100.0%)
8	37732484_01	37732484	paclitaxel	Aorta	11	10/11 (90.9%)
9	36318267_01	36318267	estradiol	Breast	8	8/8 (100.0%)
10	36553506_01	36553506	panobinostat	Brain	12	10/12 (83.3%)
11	35410383_01	35410383	Fluorouracil	Breast	6	6/6 (100.0%)
12	41871169_01	41871169	panobinostat	B lymphoblast	6	6/6 (100.0%)
13	38652658_01	38652658	ispinesib	Brain	9	8/9 (88.9%)
14	36382181_01	36382181	enzalutamide	Prostate	9	7/9 (77.8%)
15	32094658_01	32094658	latrunculin A	Pancreas	4	4/4 (100.0%)
16	38272949_02	38272949	GW3965	Brain	4	4/4 (100.0%)
17	38589664_01	38589664	cisplatin	Stomach	3	3/3 (100.0%)
18	39803533_01	39803533	TCDD	Skin	3	3/3 (100.0%)
19	40166195_01	40166195	doxorubicin	Breast	3	3/3 (100.0%)
20	34857732_01	34857732	GSK126	Prostate	8	5/8 (62.5%)

Across the 20 benchmarks there are 212 within-benchmark unique target genes, of which 195 (92.0%) match the encoded direction under the strict aggregate check described below.

Direction validation

For each target gene, the release audit compares the mean of the treated matrix (ground_truth.h5ad) with the mean of the control matrix (control.h5ad):

relative_effect = (treated_mean - control_mean) /
                  (abs(treated_mean) + abs(control_mean))

Values at least 0.1 are classified as UP, values at most -0.1 as DOWN, and intermediate values as NS. This is an aggregate dataset-level consistency check, not a dose-stratified or time-stratified statistical significance test.

H5AD content

X contains the processed expression matrix. The files also retain observation and variable metadata and, where available, a counts layer. Consult test_case.json for target genes, expected relation, perturbation groups, time groups, and cell type for each test.

Audit notes

All hard integrity checks passed. Two JSON test cases contain no target genes and are therefore not evaluable. Several JSON time/dose labels are not present as literal categorical values in obs; use the recorded condition, orig.ident, and sample_id fields together with the JSON specification. One benchmark has six barcodes shared between the separate control and treated files; use sample_id or the split name when concatenating. One benchmark stores the same gene set in a different column order between splits; downstream joins must align by var_names, never by column position.

Data leakage warning

Benchmarks derived from the same source context may not represent statistically independent samples. Keep benchmark_id and PMID grouping intact when constructing train/test splits; random cell-level splitting can cause leakage.

Citation

Each row in benchmarks.csv contains the PMID and paper title. Cite the relevant original papers when using individual benchmarks.