JBrowse: a dynamic web platform for genome visualization and analysis
By Robert M. Buels, Eric Yao, Colin M. Diesh, Richard D. Hayes, M. Munoz-Torres, G. Helt, D. Goodstein, Christine G. Elsik, Suzanna Lewis, Lincoln D. Stein and 1 more. Genome Biology, 2016
681 citations recorded by the source corpus.
JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. JBrowse is a mature web application suitable for genome visualization and analysis.
Subfields: Biomedical Engineering, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/c152e41b1f9a450ca9424b0b73c09fb14bfabac1
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Citations in the corpus
- igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV) (2020, methodology): “…such views have been provided in genome browsers, including large client-server systems such as the UCSC Genome Browser [1] and the Ensembl Genome Browser [2], rich client web applications such as JBrowse [3], and desktop applications such as the Integrative Genomics Viewer (IGV) [4,5].”
- FlyBase: a guided tour of highlighted features (2022, neutral): “The way in which high-throughput data are incorporated depends on the data type, and can involve several approaches that involve the JBrowse genome viewer (Buels et al. 2016), custom gene page data visualizations, download files, and sometimes even custom data analysis tools.”
- HTSlib: C library for reading/writing high-throughput sequencing data (2021, positive): “For example, HTSJDK is the Java equivalent [7] and is used extensively in Java applications; Sambamba [8] is written in the D language and focuses primarily on efficient multi-threaded work; Scramble [9] has BAM and SAM capability and is the primary source for experimental CRAM [10, 11] development;”
- REDIportal: a comprehensive database of A-to-I RNA editing events in humans (2016, positive): “In contrast with previous editing databases, REDIportal deploys the powerful client-side and JavaScript-based JBrowse browser (18).”