Formalizing and benchmarking open problems in single-cell genomics.
Visit the Open Problems Website.
- For contributing guidelines, see CONTRIBUTING.md
- For instructions on editing Docker images, see docker/README.md
- For instructions on using the
openproblems-cli, see openproblems/api/README.md - For a walkthrough of the GitHub Actions workflows and AWS Sagemaker, see SAGEMAKER.md
- For a description of existing an proposed tasks, see TASKS.md
- For a video introduction to this GitHub repository, watch our Repository introduction
- For a video tutorial on adding new tasks, watch our How to add a new task tutorial
Core (alphabetically):
- Daniel Burkhardt (@dburkhardt), Cellarity
- Robrecht Cannoodt (@rcannood), Data Intuitive
- Scott Gigante (@scottgigante-immunai), Immunai
- Christopher Lance (@xlancelottx), Helmholtz Munich
- Malte Luecken (@LuckyMD), Helmholtz Munich
- Angela Pisco (@aopisco), CZ Biohub
Task leaders (alphabetically):
Full tasks (>1 datasets, >5 methods):
- Batch integration - Daniel Strobl (@danielStrobl)
- Cell-cell communication - Daniel Dimitrov (@dbdimitrov)
- Dimensionality reduction - Michael Vinyard (@mvinyard) and Luke Zappia (@lazappi)
- Label projection - Nick Markov (@mxposed)
- Spatial deconvolution - Alma Anderson (@almaan) and Giovanni Palla (@giovp)
Task stubs:
- Data denoising - Wes Lewis (@weslewis)
- Multimodal data integration - The Open Problems core team
Tasks in discussion:
- ATAC denoising - Dominik Otto (@katosh)
- Differential abundance - Emma Dann (@emdann)
- Regulatory effect prediction - Qian (Alvin) Qin (@qinqian)
Supervision (alphabetically):
- Jonathan Bloom (@jbloom22)
- Smita Krishnaswamy, Yale
- Fabian Theis, Helmholtz Munich
Chan Zuckerberg Initiative Support (alphabetically):
- Jonah Cool
- Fiona Griffin
- Ivana Williams
Contributors:
See the long list of all those who contributed datasets, methods, metrics, or infrastructure code here