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© Research
Publication : Nature protocols

Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor.

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Nature protocols - 01 Aug 2021

Fischer S, Crow M, Harris BD, Gillis J,

Link to Pubmed [PMID] – 34234317

Link to DOI – 10.1038/s41596-021-00575-5

Nat Protoc 2021 08; 16(8): 4031-4067

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.

https://pubmed.ncbi.nlm.nih.gov/34234317