期刊
NATURE PROTOCOLS
卷 16, 期 8, 页码 4031-4067出版社
NATURE PORTFOLIO
DOI: 10.1038/s41596-021-00575-5
关键词
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资金
- NIH [K99MH120050, R01MH113005, R01LM012736, U19MH114821]
- CSHL Crick Cray Fellowship
The protocol introduces an efficient and robust quantification method for cell-type replicability using MetaNeighbor, which allows for identification of gene sets contributing to cell identity. The method is based on an open-source R package and can typically be run in less than 5 minutes for millions of cells.
Single-cell RNA-sequencing data have significantly advanced the characterization of cell-type diversity and composition. However, cell-type definitions vary across data and analysis pipelines, raising concerns about cell-type validity and generalizability. With MetaNeighbor, we proposed an efficient and robust quantification of cell-type replicability that preserves dataset independence and is highly scalable compared to dataset integration. In this protocol, we show how MetaNeighbor can be used to characterize cell-type replicability by following a simple three-step procedure: gene filtering, neighbor voting and visualization. We show how these steps can be tailored to quantify cell-type replicability, determine gene sets that contribute to cell-type identity and pretrain a model on a reference taxonomy to rapidly assess newly generated data. The protocol is based on an open-source R package available from Bioconductor and GitHub, requires basic familiarity with Rstudio or the R command line and can typically be run in <5 min for millions of cells. This protocol provides step-by-step instructions for using MetaNeighbor, a computational tool that allows quantification of cell-type replicability across single-cell transcriptomic datasets and identifies the gene sets that contribute to cell identity.
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