This lesson assumes you have the R, RStudio software installed on your computer.
R can be downloaded here.
RStudio is an environment for developing using R. It can be downloaded here. You will need the Desktop version for your computer.
This workshop also requires package installation from CRAN and from Bioconductor.
To install required packages from CRAN, run this code in the Console.
For diet study, install:
install.packages(pkgs = c("ggplot2", "dplyr", "tibble"))
For addiction study, install:
install.packages(pkgs = c("ggplot2", "plyr", "dplyr", "ape", "flashClust", "WGCNA"))
Alternatively, you can use the Packages tab in RStudio. Select the Packages tab and click the Install button. Type this comma-separated list of package names into the pop-up window, like this:
ggplot2, dplyr, tibble
The biocLite.R script installs Bioconductor packages.
Run the following in the R console to read this script from Bioconductor, then run the script to install required Bioconductor packages.
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
For diet study, install:
biocLite(pkgs = c("DESeq2", "limma"))
For addiction study, install:
biocLite(pkgs = c("DESeq2", "org.Mm.eg.db", "genefilter", "topGO", "DT", "biomaRt", "limma"))
Make a new folder in your Desktop called rna-seq. Move into this new folder.
Create a data folder to hold the data, a scripts folder to house your scripts, and a results folder to hold results.
Alternatively, you can use the R console to run the following commands for steps 1 and 2.
setwd("~/Desktop")
dir.create("./rna-seq")
setwd("~/Desktop/rna-seq")
dir.create("./data")
dir.create("./scripts")
dir.create("./results")
data folder.For diet study, download:
liver data for eQTL, pQTL, and mediation analyses
raw count data
For addiction study, download:
addiction data