radiaj / gcrc_session3

R code and files to run session 3 examples.

GCRC_session3

This repository contains the R code and files to run the GCRC session 3 bioinformatics workshop examples.

Instructions

Transfer your results from the STAR/ folder on the cluster to your laptop with Filezilla. If you did not run STAR or did not complete the exercise. You can download the results here in the counts/ folder.

Prior to the class, you will also need to download and install the Rstudio Dektop and R on your laptop. You will also need to install the DESeq2, RColorBrewer, and gplots R packages need to run the scripts from Bioconductor and/or CRAN.

For general information on how to install R packages from the CRAN see https://www.r-bloggers.com/how-to-install-packages-on-r-screenshots/.

To install R and RStudio Desktop

R can be downloaded for Linux, Mac and PC from https://cran.rstudio.com/. RStudio Desktop can be downloaded for Linux, Mac and PC at https://www.rstudio.com/products/rstudio/download3/.

Alternatively, you can run R on the Briaree cluster by adding the following module to your session and entering R on the terminal.

# On Briaree in the terminal enter:
module add R/3.2.1-gcc
R

To install DESeq2 (Bioconductor)

Open RStudio or start an R session on Briaree.

# In your R session enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

# Test your installation
library("DESeq2")

# If you get error messages be sure you install the missing R packages mentioned in the error message with 
# install.packages()
# or if the missing package is on Bioconductor
# source("https://bioconductor.org/biocLite.R")
# biocLite("DESeq2")

See http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html for more information on the DESeq2 package and dependencies.

To install RColorBrewer (CRAN)

install.packages("RColorBrewer")

# Test your installation
library("RColorBrewer")

To intall gplots (CRAN)

install.packages("gplots")

# Test your installation
library("gplots")