Defining and benchmarking open problems in single-cell analysis
benchmarking
scrna-seq
website
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.
Citation
BibTeX citation:
@misc{d._luecken2024,
author = {D. Luecken, Malte and Gigante, Scott and B. Burkhardt,
Daniel and Cannoodt, Robrecht and C. Strobl, Daniel and S. Markov,
Nikolay and Zappia, Luke and Palla, Giovanni and Lewis, Wesley and
Dimitrov, Daniel and E. Vinyard, Michael and Magruder, D.S. and
Andersson, Alma and Dann, Emma and Qin, Qian and J. Otto, Dominik
and Klein, Michal and Borisovna Botvinnik, Olga and Deconinck,
Louise and Waldrant, Kai and Open Problems Jamboree Members, The and
M. Bloom, Jonathan and Oliveira Pisco, Angela and Saez-Rodriguez,
Julio and Wulsin, Drausin and Pinello, Luca and Saeys, Yvan and J
Theis, Fabian and Krishnaswamy, Smita},
title = {Defining and Benchmarking Open Problems in Single-Cell
Analysis},
date = {2024-03-03},
url = {https://lazappi.id.au/publications/2024-luecken-OpenProblems/},
doi = {10.21203/rs.3.rs-4181617/v1},
langid = {en},
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.}
}
For attribution, please cite this work as:
D. Luecken, Malte, 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.” Research Square. https://doi.org/10.21203/rs.3.rs-4181617/v1.