Fast Interpolation-based t-SNE for Improved Visualization of Single-Cell RNA-Seq Data

t-distributed Stochastic Neighborhood Embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell popula...

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Autores principales: Linderman, George C., Rachh, Manas, Hoskins, Jeremy G., Steinerberger, Stefan, Kluger, Yuval
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2019
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402590/
https://www.ncbi.nlm.nih.gov/pubmed/30742040
http://dx.doi.org/10.1038/s41592-018-0308-4
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author Linderman, George C.
Rachh, Manas
Hoskins, Jeremy G.
Steinerberger, Stefan
Kluger, Yuval
author_facet Linderman, George C.
Rachh, Manas
Hoskins, Jeremy G.
Steinerberger, Stefan
Kluger, Yuval
author_sort Linderman, George C.
collection PubMed
description t-distributed Stochastic Neighborhood Embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we implement a heatmap-style visualization for scRNA-seq based on one-dimensional t-SNE for simultaneously visualizing the expression patterns of thousands of genes.
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spelling pubmed-64025902019-08-11 Fast Interpolation-based t-SNE for Improved Visualization of Single-Cell RNA-Seq Data Linderman, George C. Rachh, Manas Hoskins, Jeremy G. Steinerberger, Stefan Kluger, Yuval Nat Methods Article t-distributed Stochastic Neighborhood Embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we implement a heatmap-style visualization for scRNA-seq based on one-dimensional t-SNE for simultaneously visualizing the expression patterns of thousands of genes. 2019-02-11 2019-03 /pmc/articles/PMC6402590/ /pubmed/30742040 http://dx.doi.org/10.1038/s41592-018-0308-4 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Linderman, George C.
Rachh, Manas
Hoskins, Jeremy G.
Steinerberger, Stefan
Kluger, Yuval
Fast Interpolation-based t-SNE for Improved Visualization of Single-Cell RNA-Seq Data
title Fast Interpolation-based t-SNE for Improved Visualization of Single-Cell RNA-Seq Data
title_full Fast Interpolation-based t-SNE for Improved Visualization of Single-Cell RNA-Seq Data
title_fullStr Fast Interpolation-based t-SNE for Improved Visualization of Single-Cell RNA-Seq Data
title_full_unstemmed Fast Interpolation-based t-SNE for Improved Visualization of Single-Cell RNA-Seq Data
title_short Fast Interpolation-based t-SNE for Improved Visualization of Single-Cell RNA-Seq Data
title_sort fast interpolation-based t-sne for improved visualization of single-cell rna-seq data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402590/
https://www.ncbi.nlm.nih.gov/pubmed/30742040
http://dx.doi.org/10.1038/s41592-018-0308-4
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