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Sfaira accelerates data and model reuse in single cell genomics.

Genome Biol. 22:248 (2021)
Publ. Version/Full Text Research data DOI
Open Access Gold
Creative Commons Lizenzvertrag
Single-cell RNA-seq datasets are often first analyzed independently without harnessing model fits from previous studies, and are then contextualized with public data sets, requiring time-consuming data wrangling. We address these issues with sfaira, a single-cell data zoo for public data sets paired with a model zoo for executable pre-trained models. The data zoo is designed to facilitate contribution of data sets using ontologies for metadata. We propose an adaption of cross-entropy loss for cell type classification tailored to datasets annotated at different levels of coarseness. We demonstrate the utility of sfaira by training models across anatomic data partitions on 8 million cells.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Data Zoo ; Model Zoo ; Single-cell Genomics; Atlas
ISSN (print) / ISBN 1474-760X
e-ISSN 1465-6906
Journal Genome Biology
Quellenangaben Volume: 22, Issue: 1, Pages: , Article Number: 248 Supplement: ,
Publisher BioMed Central
Publishing Place Campus, 4 Crinan St, London N1 9xw, England
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Helmholtz AI - HMGU (HAI - HMGU)
Grants Joachim Herz Stiftung
Helmholtz Zentrum Munchen
Deutsche Forschungsgemeinschaft