Open Problems in Single-Cell Analysis
Community benchmark suite for single-cell analysis with reproducible Viash/Nextflow pipelines and NeurIPS tracks.
Kind
consortium
Composite
91.9
Benchmarks tracked
29
Direct-linked
0
As of
2026-05-12
Host organisation
CZI + Helmholtz Munich + Yale + HMS
Primary contacts
Fabian Theis, Malte Luecken, Daniel Burkhardt, Sandrine Dudoit
Founded
2021-06
License model
MIT
Official site
GitHub
Count methodology
openproblems.bio task registry + Luecken et al. Nat Biotech 2025: 29 benchmark tasks (batch integration, denoising, dim-reduction, label projection, perturbation, spatial, multimodal).
Rubric
rigor
5
coverage
5
maintenance
5
adoption
4
quality
5
accessibility
5
industry_relevance
3
Breakdown
batch_integration
3
perturbation
4
multimodal
6
label_transfer
4
spatial
5
other
7
Notes
Gold-standard single-cell benchmarking rigor; Nat Biotech 2025.