34
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

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

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          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.

          Related collections

          Most cited references18

          • Record: found
          • Abstract: not found
          • Article: not found

          A hierarchical O(N log N) force-calculation algorithm

            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions

              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              heatmaply: an R package for creating interactive cluster heatmaps for online publishing

              Abstract Summary heatmaply is an R package for easily creating interactive cluster heatmaps that can be shared online as a stand-alone HTML file. Interactivity includes a tooltip display of values when hovering over cells, as well as the ability to zoom in to specific sections of the figure from the data matrix, the side dendrograms, or annotated labels. Thanks to the synergistic relationship between heatmaply and other R packages, the user is empowered by a refined control over the statistical and visual aspects of the heatmap layout. Availability and implementation The heatmaply package is available under the GPL-2 Open Source license. It comes with a detailed vignette, and is freely available from: http://cran.r-project.org/package=heatmaply. Contact tal.galili@math.tau.ac.il Supplementary information Supplementary data are available at Bioinformatics online.
                Bookmark

                Author and article information

                Journal
                101215604
                32338
                Nat Methods
                Nat. Methods
                Nature methods
                1548-7091
                1548-7105
                26 February 2019
                11 February 2019
                March 2019
                11 August 2019
                : 16
                : 3
                : 243-245
                Affiliations
                [1 ]Applied Mathematics Program, Yale University, New Haven, CT 06511, USA
                [2 ]Department of Mathematics, Yale University, New Haven, CT 06511, USA
                [3 ]Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
                Author notes
                [* ]Corresponding author ( Yuval.Kluger@ 123456yale.edu )
                [4.]

                Author Contributions

                All authors conceived and designed the project. G.C.L. implemented the method. All authors wrote and edited the manuscript.

                Article
                NIHMS1517258
                10.1038/s41592-018-0308-4
                6402590
                30742040
                abcb8a8f-3cfc-41e1-8d5c-54f86ae2d21a

                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

                History
                Categories
                Article

                Life sciences
                Life sciences

                Comments

                Comment on this article