Visualizing Genomic Data Using Gviz and Bioconductor

Methods Mol Biol. 2016;1418:335-51. doi: 10.1007/978-1-4939-3578-9_16.

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.

Keywords: Annotation; Genomics; NGS; Visualization.

MeSH terms

  • Computational Biology / methods*
  • Databases, Genetic
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing
  • Internet
  • Molecular Sequence Annotation / methods
  • Software*