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

Etienne Becht, Charles-Antoine Dutertre, Immanuel W. H. Kwok, Lai Guan Ng, Florent Ginhoux, Evan W. Newell
doi: https://doi.org/10.1101/298430
Etienne Becht
1Singapore Immunology Network (SigN), Agency for Science, Technology and Research (A*STAR)
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Charles-Antoine Dutertre
1Singapore Immunology Network (SigN), Agency for Science, Technology and Research (A*STAR)
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Immanuel W. H. Kwok
1Singapore Immunology Network (SigN), Agency for Science, Technology and Research (A*STAR)
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Lai Guan Ng
1Singapore Immunology Network (SigN), Agency for Science, Technology and Research (A*STAR)
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Florent Ginhoux
1Singapore Immunology Network (SigN), Agency for Science, Technology and Research (A*STAR)
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Evan W. Newell
1Singapore Immunology Network (SigN), Agency for Science, Technology and Research (A*STAR)
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  • For correspondence: evan_newell@immunol.a-star.edu.sg
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Abstract

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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 10, 2018.
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Evaluation of UMAP as an alternative to t-SNE for single-cell data
Etienne Becht, Charles-Antoine Dutertre, Immanuel W. H. Kwok, Lai Guan Ng, Florent Ginhoux, Evan W. Newell
bioRxiv 298430; doi: https://doi.org/10.1101/298430
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Evaluation of UMAP as an alternative to t-SNE for single-cell data
Etienne Becht, Charles-Antoine Dutertre, Immanuel W. H. Kwok, Lai Guan Ng, Florent Ginhoux, Evan W. Newell
bioRxiv 298430; doi: https://doi.org/10.1101/298430

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