Defining and Benchmarking Open Problems in Single-Cell Analysis (2024)

This paper defines and benchmarks key open problems in single-cell analysis, providing a comprehensive overview of challenges and solutions in the field.

Luecken, M., Gigante, S., Burkhardt, D., Cannoodt, R., Strobl, D., Markov, N., Zappia, L., Palla, G., Lewis, W., Dimitrov, D., Vinyard, M., Magruder, D., Andersson, A., Dann, E., Qin, Q., Otto, D., Klein, M., Botvinnik, O., Deconinck, L.,Waldrant, K., Rieck, B., Ahlmann-Eltze, C., Beltrame, E. da V., Benz, A., González-Blas, C. B., Chen, A., DeMeo, B., Ergen, C., Floc’hlay, S., Gayoso, A., Hicks, S., Ji, Y., Kleshchevnikov, V., Manno, G. L., Lombardo, M., Lopez, R., Righelli, D., Sarkar, H., Svensson, V., Tong, A., Xing, G., Xu, C., Bloom, J., Pisco, A., Saez-Rodriguez, J., Wulsin, D., Pinello, L., Saeys, Y., Theis, F., & Krishnaswamy, S. (2024).

Defining and benchmarking open problems in single-cell analysis. Research Square Platform LLC.

This paper defines and benchmarks key open problems in single-cell analysis, providing a comprehensive overview of challenges and solutions in the field.

http://dx.doi.org/10.21203/rs.3.rs-4181617/v1

Abstract: With the growing number of single-cell analysis tools, benchmarks are increasingly important to guide analysis and method development. However, a lack of standardisation and extensibility in current benchmarks limits their usability, longevity, and relevance to the community. We present Open Problems, a living, extensible, community-guided benchmarking platform including 10 current single-cell tasks that we envision will raise standards for the selection, evaluation, and development of methods in single-cell analysis.

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