So, to make things easier for our https://github.com/HCBravoLab/workshopBioc2016 at http://bioconductor.org/help/course-materials/2016/BioC2016/ we made a few changes to epivizr (last night...) so that the standalone version runs within the Rstudio Viewer pane (yay!).
Since we made these changes after course AMI was setup, we need a couple of things before we get going. Follow these instructions and we should be good to go:
# update epivizr
biocLite("epiviz/epivizr", build_vignettes=TRUE)
# install epivizrStandalone
biocLite("epiviz/epivizrStandalone", build_vignettes=TRUE)
# install this package
biocLite("hcbravolab/bioc2016addendum", build_vignettes=TRUE, dependencies=TRUE)From there we can follow the vignette in this package to setup the epiviz workspaces we will use throughout the workshop (my preffered way is to use
file.edit(system.file("doc","Bioc2016Addendum.Rmd", package="bioc2016Addendum"))