igvR is an R package providing interactive connections to igv.js (the Integrative Genomics Viewer) running in a web browser.
I am grateful to Jim Robinson, Helga Thorvaldsdóttir, Douglass Turner and colleagues for their fine work in igv.js, and their unfailing responsiveness to all requests and questions.
igvR is based upon the Bioconductor R package BrowserViz - of which it is a subclass. It offers easy interactive visual exploration of genomic data from R:
Here, for example, we display a BAM pileup from a ChIP-Seq experiment, accompanied by narrow peaks called by MACS2, and TF motif matches from MotifDb to sequence scored by the Bioconductor’s Biostrings::matchPWM, and showing a browser popup with the motif logo associated with the transcription factor CTCF, obtained by clicking on a region displayed in the lowest track.
Code for this example is in the vignette titled
"Explore ChIP-seq alignments from a bam file, MACS2 narrowPeaks, conservation, methylation and motif matching"