JBrowseR: an R interface to the JBrowse 2 genome browser

MOTIVATION: Genome browsers are an essential tool in genome analysis. Modern genome browsers enable complex and interactive visualization of a wide variety of genomic data modalities. While such browsers are very powerful, they can be challenging to configure and program for bioinformaticians lackin...

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Detalles Bibliográficos
Autores principales: Hershberg, Elliot A, Stevens, Garrett, Diesh, Colin, Xie, Peter, De Jesus Martinez, Teresa, Buels, Robert, Stein, Lincoln, Holmes, Ian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8570803/
https://www.ncbi.nlm.nih.gov/pubmed/34196689
http://dx.doi.org/10.1093/bioinformatics/btab459
Descripción
Sumario:MOTIVATION: Genome browsers are an essential tool in genome analysis. Modern genome browsers enable complex and interactive visualization of a wide variety of genomic data modalities. While such browsers are very powerful, they can be challenging to configure and program for bioinformaticians lacking expertise in web development. RESULTS: We have developed an R package that provides an interface to the JBrowse 2 genome browser. The package can be used to configure and customize the browser entirely with R code. The browser can be deployed from the R console, or embedded in Shiny applications or R Markdown documents. AVAILABILITY AND IMPLEMENTATION: JBrowseR is available for download from CRAN, and the source code is openly available from the Github repository at https://github.com/GMOD/JBrowseR/.

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