JBrowseR: an R interface to the JBrowse 2 genome browser-Reference-Cited by-同舟云学术

JBrowseR: an R interface to the JBrowse 2 genome browser

Published:2021-07-01 Issue:21 Volume:37 Page:3914-3915
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Hershberg Elliot A¹^ORCID,Stevens Garrett¹^ORCID,Diesh Colin¹,Xie Peter¹,De Jesus Martinez Teresa¹,Buels Robert¹,Stein Lincoln²,Holmes Ian¹

Affiliation:

1. Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA

2. Adaptive Oncology, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada

Abstract

Abstract 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/.

Funder

NIH

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

http://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab459/39771578/btab459.pdf

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