Interactive Genome Browser in R
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.
See my attempt at https://github.com/Marlin-Na/TnT
Details of your coding project
- Provide functions to link R with tnt genome, tnt tooltip and if possible, tnt tree.
- Provide user-interfacing functions that transform R data types (e.g. GRanges) and create valid genome browser.
- Write documentations and vignettes.
- Headless browser tests using RSelenium (we use this in animint) or seleniumPipes. Both are for headless browser testing, but RSelenium is more stable.
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.
- Miguel Pignatelli <email@example.com> is the author of TnT libraries and willing to mentor this project.
- Toby Dylan Hocking <firstname.lastname@example.org> is willing to mentor this project.
Solutions of tests
Students, please post a link to your test results here.