In uhlitz/dallianceR: A grammar of genome browsing with dalliance

library(dallianceR)

This is a sketch for a htmlwidget wrapper for JavScript genome browser dalliance.

Quick guide

A dalliance function call generates a genome browser htmlwidget with a given reference genome (eg. GRCh38) and a given gene annotation (eg. GENCODEv21):

library(dallianceR)
library(DT)
library(dplyr)

Example browser with tracks

dalliance(data = dummy)

datatable(data_frame(a = 1:10, b = runif(10)))

Workflow

A common workflow loads...

• a public reference genome (via DAS)
• a public gene annotation (via DAS)
• custom tracks with
  • quantitative data: .bigbed, .bigwig or indexed .bam.
  • or qualitative data: eg. .gff and .vcf (future)

Where grouped tracks should be added in lists. In general, syntax to build a genome browser could resemble the leaflet syntax to build maps.

dalliance %>% 
  addReference("GRCh38") %>% 
  addAnnotation("GENCODEv21") %>% 
  addTrack(list("my_track_A_rep1", "my_track_A_rep2"), 
            list("my_track_B_rep1", "my_track_B_rep2")) %>% 

uhlitz/dallianceR documentation built on May 3, 2019, 2:22 p.m.