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Evaluation of UMAP as an alternative to t-SNE for single-cell data

By Etienne Becht, Charles-Antoine Dutertre, Immanuel W. H. Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell

Posted 10 Apr 2018
bioRxiv DOI: 10.1101/298430 (published DOI: 10.1038/nbt.4314)

Uniform Manifold Approximation and Projection (UMAP) is a recently-published non-linear dimensionality reduction technique. Another such algorithm, t-SNE, has been the default method for such task in the past years. Herein we comment on the usefulness of UMAP high-dimensional cytometry and single-cell RNA sequencing, notably highlighting faster runtime and consistency, meaningful organization of cell clusters and preservation of continuums in UMAP compared to t-SNE.

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