Section outline

  • Participants must bring a laptop and install the following:

    • 64-bit Java 8
    • the latest version of the R, R Studio and Cytoscape software installed.
    • the R package WGCNA and some Bioconductor packages that are used by WGCNA using these commands:
      source("http://bioconductor.org/biocLite.R")
      biocLite(c("AnnotationDbi", "impute", "GO.db", "preprocessCore"))
      install.packages(c("gtable", "munsell", "plyr", "RColorBrewer", "stringr","digest"))
      install.packages(c("matrixStats", "Hmisc", "splines", "foreach", "doParallel", "fastcluster", "dynamicTreeCut", "survival"))
      install.packages("WGCNA")
    R package: SNFtool
    1) Download either the source (Linux) or Mac OSX/Windows binaries from the CRAN directory:
    SNFtool_2.2.zip (Windows)
    SNFtool_2.2.tgz (OSX)
    SNFtool_2.2.tar.gz (Linux)
    2) Launch R and install the required package heatmap.plus

    R
    install.packages("heatmap.plus")
    # Exit R

    3) Unzip/unpack the archive and move SNFtool folder to a new directory

    For MacOSX/Windows:
    unzip SNFtool_2.2.tgz 
    or
    unzip SNFtool_2.2.zip
    R CMD INSTALL SNFtool
    For Linux:
    tar -vxzf SNFtool_2.2.tar.gz
    R CMD INSTALL SNFtool

    4) Launch R and load the library
    library("SNFtool”)

    RStudio with Markdown
    1) Download and install RStudio from https://www.rstudio.com/
    2) Install Markdown package
    Launch RStudio
    install.packages("markdown")