scmap – projection of single-cell RNA-seq data across data sets

Single-cell RNA-seq (scRNA-seq) allows researchers to define cell types on the basis of unsupervised clustering of the transcriptome. However, differences in experimental methods and computational analyses make it challenging to compare data across experiments. Wellcome Sanger Institute researchers present scmap, a method for projecting cells from an scRNA-seq data set onto cell types or individual cells from other experiments.


scmap can map individual cells from a query sample to cell types in the reference (scmap-cluster; solid lines) or to individual cells in a reference (scmap-cell; dashed lines). Colors correspond to previously identified cell types; gray denotes unknown cell types.

Availability web version at

Kiselev VY, Yiu A, Hemberg M. (2018) scmap: projection of single-cell RNA-seq data across data sets. Nat Methods [Epub ahead of print]. [abstract]

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