Links

Shiny

Shiny

Shiny Server

DT (DataTables in R)

Bioconductor

Bioconductor cheat sheet

Gviz (and see also ggbio)

This is a tutorial prepared by the Monash Bioinformatics Platform on the Shiny library developed by RStudio, to be presented as part of a hands on workshop as part of ABACBS 2016 and bioCasia2016. Shiny provides an easy way to present R data analysis interactively and over the web.

Setup

Before the tutorial please install R and RStudio,

then install packages from CRAN and Bioconductor with the following R code:

install.packages("shiny")
install.packages("DT")

source("https://bioconductor.org/biocLite.R")
biocLite(c(
    "BSgenome.Scerevisiae.UCSC.sacCer3",
    "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene",
    "GenomicRanges",
    "rtracklayer",
    "Gviz"))

Make sure you are running R 3.3 and Bioconductor 3.3, or higher.

# To upgrade an old Bioconductor installation
source("https://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")

Files

Download these files. tutorial.R contains all the code in the “tutorial” link below. During the tutorial, we will be stepping through tutorial.R in RStudio. I’m still making changes to tutorial.R, so please download it on the day!

Content

Source code