Fischer, Stephan, Crow, Megan, Harris, Benjamin D, Gillis, Jesse (July 2021) Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor. Nature Protocols. ISSN 1754-2189
Abstract
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.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > animal organs, tissues, organelles, cell types and functions > organs types and functions > brain bioinformatics > computational biology organism description > animal > mammal organism description > animal > mammal > rodent > mouse organs, tissues, organelles, cell types and functions > organs types and functions organs, tissues, organelles, cell types and functions organism description > animal > mammal > rodent bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes |
| CSHL Authors: | |
| Communities: | CSHL labs > Gillis Lab School of Biological Sciences > Publications |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 7 July 2021 |
| Date Deposited: | 09 Jul 2021 13:57 |
| Last Modified: | 23 Jan 2024 20:05 |
| PMCID: | PMC8826496 |
| URI: | https://repository.cshl.edu/id/eprint/40265 |
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