devtools::install_github(repo="BioinformaticsFMRP/TCGAbiolinks")

devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")
source("https://bioconductor.org/biocLite.R")
biocLite(c("pathview","clusterProfiler","ELMER"))
install.packages(c("shiny","readr","googleVis","shinydashboard"))
devtools::install_github("thomasp85/shinyFiles")
devtools::install_github("ebailey78/shinyBS", ref="shinyBS3")
devtools::install_github("daattali/shinyjs")
install.packages("~/TCGAbiolinksGUI_0.99.0_R_x86_64-pc-linux-gnu.tar.gz", repos = NULL, type = "source")

library(TCGAbiolinks)

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

## Temporary procedure to have TCGAbiolinksGUI working (solution for the Error : object ‘TCGAquery’ is not exported by 'namespace:TCGAbiolinks')

# On MAC OSx (10.11.6)
# Bioconductor 3.4 (BiocInstaller 1.24.0)
# R version 3.3.2 (2016-10-31)

# You need to have TCGAbiolinks installed from Bioconductor 

# Remove the TCGAbiolinks installed by:
# remove.packages("TCGAbiolinks")
# Or remove it from your R folder by terminal
# rm -r /Library/Frameworks/R.framework/Versions/3.3/Resources/library/TCGAbiolinks
# Install TCGAbiolinks from bioconductor 

source("https://bioconductor.org/biocLite.R")
biocLite("TCGAbiolinks")

# Load all required packages
require(TCGAbiolinks)
require(pathview)
require(ELMER)

# Install and load the required packages

biocLite(c("clusterProfiler"))
require(clusterProfiler)

biocLite(c("colourpicker"))
require(colourpicker)

# Install TCGAbiolinksGUI from local package (the package is located on Dropbox in /2016_11_22_TCGACARD/packages )

# You can obtain TCGAbiolinksGUI package from here
# https://www.dropbox.com/sh/gds76erukn46lu9/AADv9TlkJWYlR1r7MgSCGdK-a?dl=0

install.packages("~/Downloads/TCGAbiolinksGUI_0.99.3.tar.gz", repos = NULL, type = "source")

# Load and run TCGAbiolinksGUI

require("TCGAbiolinksGUI")
TCGAbiolinksGUI()