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JBrowseR: an R interface to the JBrowse 2 genome browser
Elliot A Hershberg1, Garrett Stevens1, Colin Diesh1
1Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.
Bioinformatics (Oxford, England)
|July 1, 2021
Summary
Bioinformaticians can now easily configure genome browsers using R code with the new JBrowseR package. This tool simplifies complex genomic data visualization, making it accessible without web development expertise.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Genome browsers are crucial for analyzing genomic data.
- Configuring and programming genome browsers often requires web development skills, posing a challenge for bioinformaticians.
- Existing genome browsers can be difficult to customize for specific research needs.
Purpose of the Study:
- To develop an R package providing an interface to the JBrowse 2 genome browser.
- To enable bioinformaticians to configure and customize genome browsers using R code.
- To facilitate the deployment of JBrowse 2 within R environments.
Main Methods:
- Development of an R package, JBrowseR, as an interface to JBrowse 2.
- Utilizing R code for browser configuration and customization.
- Integration capabilities with R console, Shiny applications, and R Markdown documents.
Main Results:
- JBrowseR allows for complete browser configuration and customization via R code.
- The package enables deployment directly from the R console.
- JBrowseR can be seamlessly embedded into Shiny applications and R Markdown documents.
Conclusions:
- JBrowseR simplifies genome browser customization for bioinformaticians.
- The package lowers the barrier to entry for advanced genomic data visualization.
- JBrowseR enhances the utility of genome browsers within the R ecosystem.
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