- Author
- Malte D. Luecken, Scott Gigante, Daniel B. Burkhardt, Robrecht Cannoodt (UGent) , Daniel C. Strobl, Nikolay S. Markov, Luke Zappia, Giovanni Palla, Wesley Lewis, Daniel Dimitrov, Michael E. Vinyard, Daniel S. Magruder, Alma Andersson, Emma Dann, Qian Qin, Dominik J. Otto, Michal Klein, Olga Borisovna Botvinnik, Louise Deconinck (UGent) , Kai Waldrant, [ missing ] The Open Problems Jamboree Members, Bastian Rieck, Constantin Ahlmann-Eltze, Eduardo da Veiga Beltrame, Andrew Benz, Carmen Bravo González-Blas, Ann Chen, Benjamin DeMeo, Can Ergen, Swann Floc'hlay, Adam Gayoso, Stephanie Hicks, Yuge Ji, Vitalii Kleshchevnikov, Gioele La Manno, Maximilian Lombardo, Romain Lopez, Dario Righelli, Hirak Sarkar, Valentine Svensson, Alexander Tong, Galen Xing, Chenling Xu, Jonathan M. Bloom, Angela Oliveira Pisco, Julio Saez-Rodriguez, Drausin Wulsin, Luca Pinello, Yvan Saeys (UGent) , Fabian J. Theis and Smita Krishnaswamy
- Organization
- Project
- 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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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01HYX1WY4DYYQ3E09ZE78472MA
- MLA
- Luecken, Malte D., et al. “Defining and Benchmarking Open Problems in Single-Cell Analysis.” NATURE PORTFOLIO, 2024, doi:10.21203/rs.3.rs-4181617/v1.
- APA
- Luecken, M. D., Gigante, S., Burkhardt, D. B., Cannoodt, R., Strobl, D. C., Markov, N. S., … Krishnaswamy, S. (2024). Defining and benchmarking open problems in single-cell analysis. https://doi.org/10.21203/rs.3.rs-4181617/v1
- Chicago author-date
- Luecken, Malte D., Scott Gigante, Daniel B. Burkhardt, Robrecht Cannoodt, Daniel C. Strobl, Nikolay S. Markov, Luke Zappia, et al. 2024. “Defining and Benchmarking Open Problems in Single-Cell Analysis.” NATURE PORTFOLIO. https://doi.org/10.21203/rs.3.rs-4181617/v1.
- Chicago author-date (all authors)
- Luecken, Malte D., Scott Gigante, Daniel B. Burkhardt, Robrecht Cannoodt, Daniel C. Strobl, Nikolay S. Markov, Luke Zappia, Giovanni Palla, Wesley Lewis, Daniel Dimitrov, Michael E. Vinyard, Daniel S. Magruder, Alma Andersson, Emma Dann, Qian Qin, Dominik J. Otto, Michal Klein, Olga Borisovna Botvinnik, Louise Deconinck, Kai Waldrant, [ missing ] The Open Problems Jamboree Members, Bastian Rieck, Constantin Ahlmann-Eltze, Eduardo da Veiga Beltrame, Andrew Benz, Carmen Bravo González-Blas, Ann Chen, Benjamin DeMeo, Can Ergen, Swann Floc’hlay, Adam Gayoso, Stephanie Hicks, Yuge Ji, Vitalii Kleshchevnikov, Gioele La Manno, Maximilian Lombardo, Romain Lopez, Dario Righelli, Hirak Sarkar, Valentine Svensson, Alexander Tong, Galen Xing, Chenling Xu, Jonathan M. Bloom, Angela Oliveira Pisco, Julio Saez-Rodriguez, Drausin Wulsin, Luca Pinello, Yvan Saeys, Fabian J. Theis, and Smita Krishnaswamy. 2024. “Defining and Benchmarking Open Problems in Single-Cell Analysis.” NATURE PORTFOLIO. doi:10.21203/rs.3.rs-4181617/v1.
- Vancouver
- 1.Luecken MD, Gigante S, Burkhardt DB, Cannoodt R, Strobl DC, Markov NS, et al. Defining and benchmarking open problems in single-cell analysis. NATURE PORTFOLIO. 2024.
- IEEE
- [1]M. D. Luecken et al., “Defining and benchmarking open problems in single-cell analysis,” NATURE PORTFOLIO. 2024.
@misc{01HYX1WY4DYYQ3E09ZE78472MA,
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.}},
author = {{Luecken, Malte D. and Gigante, Scott and Burkhardt, Daniel B. and Cannoodt, Robrecht and Strobl, Daniel C. and Markov, Nikolay S. and Zappia, Luke and Palla, Giovanni and Lewis, Wesley and Dimitrov, Daniel and Vinyard, Michael E. and Magruder, Daniel S. and Andersson, Alma and Dann, Emma and Qin, Qian and Otto, Dominik J. and Klein, Michal and Botvinnik, Olga Borisovna and Deconinck, Louise and Waldrant, Kai and The Open Problems Jamboree Members, [ missing ] and Rieck, Bastian and Ahlmann-Eltze, Constantin and Beltrame, Eduardo da Veiga and Benz, Andrew and González-Blas, Carmen Bravo and Chen, Ann and DeMeo, Benjamin and Ergen, Can and Floc'hlay, Swann and Gayoso, Adam and Hicks, Stephanie and Ji, Yuge and Kleshchevnikov, Vitalii and Manno, Gioele La and Lombardo, Maximilian and Lopez, Romain and Righelli, Dario and Sarkar, Hirak and Svensson, Valentine and Tong, Alexander and Xing, Galen and Xu, Chenling and Bloom, Jonathan M. and Pisco, Angela Oliveira and Saez-Rodriguez, Julio and Wulsin, Drausin and Pinello, Luca and Saeys, Yvan and Theis, Fabian J. and Krishnaswamy, Smita}},
language = {{eng}},
pages = {{24}},
series = {{NATURE PORTFOLIO}},
title = {{Defining and benchmarking open problems in single-cell analysis}},
url = {{http://doi.org/10.21203/rs.3.rs-4181617/v1}},
year = {{2024}},
}
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