This repository has been superseded by openproblems-v2.

Open Problems in Single-Cell Analysis

Formalizing and benchmarking open problems in single-cell genomics.

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):

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:

Tasks in discussion:

Supervision (alphabetically):

Chan Zuckerberg Initiative Support (alphabetically):

Contributors:

See the long list of all those who contributed datasets, methods, metrics, or infrastructure code here