Prerequisites

[Scott Newman]

Installing R and R Packages

Shiny CGH is written in R and requires several packages to be installed from CRAN and Bioconductor.

1) Download and install R: http://www.r-project.org/
2) Windows users may need to install a Perl interpretor http://www.activestate.com/activeperl
3) Start R and install the following packages:

Bioconductor

http://www.bioconductor.org/install/
source("http://bioconductor.org/biocLite.R")
biocLite()

cghMCR

http://www.bioconductor.org/packages/2.12/bio/html/cghMCR.html
source("http://bioconductor.org/biocLite.R")
biocLite("cghMCR")

CNTools

http://www.bioconductor.org/packages/release/bioc/html/CNTools.html
source("http://bioconductor.org/biocLite.R")
biocLite("CNTools")

GenomicRanges

http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")

Shiny

http://cran.r-project.org/web/packages/shiny/index.html
install.packages(“shiny”)

ggplot2

http://cran.r-project.org/web/packages/ggplot2/index.html
install.packages(“ggplot2”)

shinyapps

https://github.com/rstudio/shinyapps
if (!require("devtools"))
install.packages("devtools")
devtools::install_github("rstudio/shinyapps")