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Statistical Genomics pp 335–351Cite as

Visualizing Genomic Data Using Gviz and Bioconductor

Part of the Methods in Molecular Biology book series (MIMB,volume 1418)

Abstract

The Gviz package offers a flexible framework to visualize genomic data in the context of a variety of different genome annotation features. Being tightly embedded in the Bioconductor genomics landscape, it nicely integrates with the existing infrastructure, but also provides direct data retrieval from external sources like Ensembl and UCSC and supports most of the commonly used annotation file types. Through carefully chosen default settings the package greatly facilitates the production of publication-ready figures of genomic loci, while still maintaining high flexibility due to its ample customization options.

Key words

  • Visualization
  • Genomics
  • NGS
  • Annotation

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Author information

Authors and Affiliations

  1. Novartis Institute for Biomedical Research, WKL-135.P18, Klybeckstrasse 141, 4057, Basel, Switzerland

    Florian Hahne

  2. Department of Biomedicine, University of Basel, Basel, Switzerland

    Robert Ivanek

Authors
  1. Florian Hahne
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  2. Robert Ivanek
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Corresponding author

Correspondence to Florian Hahne .

Editor information

Editors and Affiliations

  1. Ohio State University, Biomed Informatics, College of Medicine, Columbus, Ohio, USA

    Ewy Mathé

  2. National Cancer Institute, National Institutes of Health, Columbia, Maryland, USA

    Sean Davis

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Hahne, F., Ivanek, R. (2016). Visualizing Genomic Data Using Gviz and Bioconductor. In: Mathé, E., Davis, S. (eds) Statistical Genomics. Methods in Molecular Biology, vol 1418. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3578-9_16

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  • DOI: https://doi.org/10.1007/978-1-4939-3578-9_16

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3576-5

  • Online ISBN: 978-1-4939-3578-9

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