CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations DOI Creative Commons

Zhirui Hu,

Pawel F. Przytycki, Katherine S. Pollard

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 17, 2024

CellWalker2 is a graph diffusion-based method for single-cell genomics data integration. It extends the CellWalker model by incorporating hierarchical relationships between cell types, providing estimates of statistical significance, and adding structures analyzing multi-omics so that gene expression open chromatin can be jointly modeled. Our open-source software enables users to annotate cells using existing ontologies probabilistically match types two or more contexts, including across species. also map genomic regions ontologies, enabling precise annotation elements derived from bulk data, such as enhancers, genetic variants, sequence motifs. Through simulation studies, we show performs better than methods in type mapping. We then use brain immune system demonstrate CellWalker2's ability discover type-specific regulatory programs both conserved divergent complex tissues.

Язык: Английский

CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations DOI Creative Commons

Zhirui Hu,

Pawel F. Przytycki, Katherine S. Pollard

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 17, 2024

CellWalker2 is a graph diffusion-based method for single-cell genomics data integration. It extends the CellWalker model by incorporating hierarchical relationships between cell types, providing estimates of statistical significance, and adding structures analyzing multi-omics so that gene expression open chromatin can be jointly modeled. Our open-source software enables users to annotate cells using existing ontologies probabilistically match types two or more contexts, including across species. also map genomic regions ontologies, enabling precise annotation elements derived from bulk data, such as enhancers, genetic variants, sequence motifs. Through simulation studies, we show performs better than methods in type mapping. We then use brain immune system demonstrate CellWalker2's ability discover type-specific regulatory programs both conserved divergent complex tissues.

Язык: Английский

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