wes-lewis/singlecellopenproblems

Formalizing and benchmarking open problems in single-cell genomics

Open Problems in Single-Cell Analysis

Formalizing and benchmarking open problems in single-cell genomics.

Visit the Open Problems Website.

Guides

• 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

The team

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