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Supervised classification enables rapid annotation of cell atlases

View ORCID ProfileHannah A. Pliner, View ORCID ProfileJay Shendure, View ORCID ProfileCole Trapnell
doi: https://doi.org/10.1101/538652
Hannah A. Pliner
1Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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Jay Shendure
1Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
2Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
3Howard Hughes Medical Institute, Seattle, WA 98195, USA
4Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
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Cole Trapnell
1Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
2Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
4Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
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ABSTRACT

Single cell technologies for profiling tissues or even entire organisms are rapidly being adopted. However, the manual process by which cell types are typically annotated in the resulting data is labor-intensive and increasingly rate-limiting for the field. Here we describe Garnett, an algorithm and accompanying software for rapidly annotating cell types in scRNA-seq and scATAC-seq datasets, based on an interpretable, hierarchical markup language of cell type-specific genes. Garnett successfully classifies cell types in tissue and whole organism datasets, as well as across species.

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Posted February 25, 2019.
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Supervised classification enables rapid annotation of cell atlases
Hannah A. Pliner, Jay Shendure, Cole Trapnell
bioRxiv 538652; doi: https://doi.org/10.1101/538652
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Supervised classification enables rapid annotation of cell atlases
Hannah A. Pliner, Jay Shendure, Cole Trapnell
bioRxiv 538652; doi: https://doi.org/10.1101/538652

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