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1.
Res Sq ; 2024 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-38645152

RESUMO

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.

2.
Nat Commun ; 12(1): 3942, 2021 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-34168133

RESUMO

We present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimulating development and testing of computational methods. We demonstrate its potential for spearheading computational methods on three applications: aligning cell developmental trajectories, cell-specific regulatory network inference and estimation of RNA velocity.


Assuntos
Simulação por Computador , Redes Reguladoras de Genes , Análise de Célula Única/métodos , Algoritmos , Benchmarking , Biologia Computacional/métodos , Perfilação da Expressão Gênica
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