Literature DB >> 34596551

Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization.

Sehi L'Yi, Qianwen Wang, Fritz Lekschas, Nils Gehlenborg.   

Abstract

The combination of diverse data types and analysis tasks in genomics has resulted in the development of a wide range of visualization techniques and tools. However, most existing tools are tailored to a specific problem or data type and offer limited customization, making it challenging to optimize visualizations for new analysis tasks or datasets. To address this challenge, we designed Gosling-a grammar for interactive and scalable genomics data visualization. Gosling balances expressiveness for comprehensive multi-scale genomics data visualizations with accessibility for domain scientists. Our accompanying JavaScript toolkit called Gosling.js provides scalable and interactive rendering. Gosling.js is built on top of an existing platform for web-based genomics data visualization to further simplify the visualization of common genomics data formats. We demonstrate the expressiveness of the grammar through a variety of real-world examples. Furthermore, we show how Gosling supports the design of novel genomics visualizations. An online editor and examples of Gosling.js, its source code, and documentation are available at https://gosling.js.org.

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Year:  2021        PMID: 34596551      PMCID: PMC8826597          DOI: 10.1109/TVCG.2021.3114876

Source DB:  PubMed          Journal:  IEEE Trans Vis Comput Graph        ISSN: 1077-2626            Impact factor:   4.579


  70 in total

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Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  The Ensembl genome database project.

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Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  TenniVis: Visualization for Tennis Match Analysis.

Authors:  Tom Polk; Jing Yang; Yueqi Hu; Ye Zhao
Journal:  IEEE Trans Vis Comput Graph       Date:  2014-12       Impact factor: 4.579

4.  A Declarative Rendering Model for Multiclass Density Maps.

Authors:  Jaemin Jo; Frederic Vernier; Pierre Dragicevic; Jean-Daniel Fekete
Journal:  IEEE Trans Vis Comput Graph       Date:  2018-08-20       Impact factor: 4.579

5.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

6.  The 4D nucleome project.

Authors:  Job Dekker; Andrew S Belmont; Mitchell Guttman; Victor O Leshyk; John T Lis; Stavros Lomvardas; Leonid A Mirny; Clodagh C O'Shea; Peter J Park; Bing Ren; Joan C Ritland Politz; Jay Shendure; Sheng Zhong
Journal:  Nature       Date:  2017-09-13       Impact factor: 49.962

7.  Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

Authors:  Ryan Lister; Ronan C O'Malley; Julian Tonti-Filippini; Brian D Gregory; Charles C Berry; A Harvey Millar; Joseph R Ecker
Journal:  Cell       Date:  2008-05-02       Impact factor: 41.582

8.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

9.  ATOM: A Grammar for Unit Visualizations.

Authors:  Deokgun Park; Steven Mark Drucker; Roland Fernandez; Niklas Elmqvist
Journal:  IEEE Trans Vis Comput Graph       Date:  2017-12-21       Impact factor: 4.579

10.  ggbio: an R package for extending the grammar of graphics for genomic data.

Authors:  Tengfei Yin; Dianne Cook; Michael Lawrence
Journal:  Genome Biol       Date:  2012-08-31       Impact factor: 13.583

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  2 in total

1.  Productive visualization of high-throughput sequencing data using the SeqCode open portable platform.

Authors:  Enrique Blanco; Mar González-Ramírez; Luciano Di Croce
Journal:  Sci Rep       Date:  2021-10-01       Impact factor: 4.379

2.  SODA: a TypeScript/JavaScript library for visualizing biological sequence annotation.

Authors:  Jack W Roddy; George T Lesica; Travis J Wheeler
Journal:  NAR Genom Bioinform       Date:  2022-10-06
  2 in total

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