igvR: Interactive Genome Exploration From R

igvR: Interactive Genome Exploration From R

Author(s): Paul T Shannon

Affiliation(s): Institute for Systems Biology

Genomic and epigenomic assays provide large quantities of many kinds of data, many of which are annotations upon the genome: alignments, variants, methylation, copy number, transcription factor binding sites to name a few. An interactive visual interface to these data is an indispensable element of exploratory data analysis. The R/Bioconductor package igvR brings all of the capabilities of the browser-based Javascript library igv.js to the computational and data-rich R programming and analysis environment. igvR is built on top of the R-to-web-browser web socket communication package BrowserViz. With igvR, two interactive exploratory environments are linked, with R commands and functions controlling, and able to query, the genome display. The related package igvShiny will be mentioned also.

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