Workshop

Software RequirementsYou will need to install R from http://cran.r-project.org/ onto your computer. We've tested the workflow on R version 3.4.1.You will also need RStudio from http://www.rstudio.com/products/rstudio/download/.After installing, open RStudio, which opens an R session, and paste in the following commands into the Console window. Hitting enter will execute the lines.source("https://bioconductor.org/biocLite.R")biocLite("biomaRt")biocLite("DESeq2")biocLite("org.Dr.eg.db")biocLite("topGO")biocLite("tximport")install.packages("rbokeh")install.packages("readr")install.packages("rjson")Once installed, scripts will be able to utilize the libraries via loading which occurs each time you execute a given workflow or script. In our case, that environment loads in the following section:library("readr")library("rjson")library("tximport")library("DESeq2")library("biomaRt")library("rbokeh")library("topGO")library("org.Dr.eg.db")These lines should execute without error. If you encounter an error like:> Error in library("topGO") : there is no package called ‘topGO’Then that package failed to install and you can retry its from above:biocLite("topGO")And read the console for any prompts.Other DownloadsDownload the osu-workshop.zip file and extract. This contains the data, some intermediate data, our working examples for this workshop. The hands-on portion will be going through the DE.Rmd document in RStudio.