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Interactive Genome Browser in R

Toby Dylan Hocking edited this page Feb 6, 2017 · 4 revisions

Background

A common task in bioinformatics is to provide visualization of genomic features along genomic coordinates, using an interactive genome browser or a static graph. Commonly used genome browser include browser-based UCSC Genome Browser, Ensembl, JBrowse, and Integrative Genomics Viewer (IGV) which runs on a local computer.

In R, the bioconductor project provided lots of packages handling genomic data and there are also packages to provide such visualization using static graphs, for example, the Gviz and ggbio packages. However, in terms of interactive data presentation and exploratory research, it would be great if we can provide a R package that wraps an javascript library for genomic visulization using htmlwidgets and provide linkage to common genomic data type defined in bioconductor.

TnT is a set of javascript libraries for visualizing trees and track-based annotations, which can be used to create a simple genome browser. It has a flexible low level api and I consider it suitable for embedding into R.

See my attempt at https://github.com/Marlin-Na/TnT

Related work

Gviz and ggbio are bioconductor packages to provide static graphs for genomic data.

Details of your coding project

  1. Provide functions to link R with tnt genome, tnt tooltip and if possible, tnt tree.
  2. Provide user-interfacing functions that transform R data types (e.g. GRanges) and create valid genome browser.
  3. Write documentations and vignettes.
  4. Headless browser tests using RSelenium (we use this in animint) or seleniumPipes. Both are for headless browser testing, but RSelenium is more stable.

Expected impact

This package will be particularly useful for exploary genome visualization and interactive genomic data presentation in R. Especially, it can be combined with Rmarkdown or shiny to build interactive documents or websites.

Mentors

  • Miguel Pignatelli <emepyc@gmail.com> is the author of TnT libraries and willing to mentor this project.
  • Toby Dylan Hocking <tdhock5@gmail.com> is willing to mentor this project.

Tests

NA

Solutions of tests

Students, please post a link to your test results here.

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