Sfaira accelerates data and model reuse in single cell genomics

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.

Automated summary

sfaira is a single-cell data zoo paired with executable pre-trained models for public datasets, addressing issues with independent analysis and contextualization in single-cell RNA-seq datasets. We propose an adaptation of cross-entropy loss for cell type classification tailored to datasets annotated at different levels of coarseness.