Synapse Setup

To participate in this workshop, you will need to have a registered Synapse account and accept the AD Knowledge Portal data terms of use.

1. If you have successfully created a Synapse account and are logged into Synapse, you should be able to view and download this file: https://www.synapse.org/#!Synapse:syn26200396
2. If you have successfully accepted the AD Portal terms of use, you should be able to view and download this file: https://www.synapse.org/#!Synapse:syn22103212

If you can access the first file, but not the second, click on the “Request Access” link next to the yellow lock icon and accept the AD Portal terms of use. Refresh the page, and you should be able to access the second file.

Software Installation

Installing the software may take up to 30 minutes. You may also need to contact your local Information Technology Help Desk to get permission or assistance installing the software. Please do this before the workshop. We will not delay the start of the course while you install software. We will help you in advance to make sure that you have everything that you need.

If you do not already have R and RStudio installed, download and install the following software:

1. R/4.3.0: Select the installation for your operating system (Windows, Mac, or Linux).
2. RStudio: Download the free Rstudio Desktop.

You do not need to install this exact version of R, but it would be good to make sure your R is relatively recent (say, updated within the past year).

Once you have installed R and RStudio, open RStudio to verify that the installation was successful.

R Library Installation

In RStudio, copy and paste the following commands into the Console:

# install synapser
install.packages("synapser", repos = c("http://ran.synapse.org", "http://cran.fhcrc.org"))

# install other required packages
install.packages(c("tidyverse", "cowplot"), dependencies = TRUE)

We will also use the BioconductoR package manager to install specific packages.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
    
BiocManager::install(c("biomaRt", "AnnotationDbi", "GO.db", "org.Mm.eg.db", "org.Hs.eg.db", "clusterProfiler", "DESeq2", "EnhancedVolcano"))

Once the installation has finished, copy and paste the following commands into the console to verify that all packages installed correctly.

library(tidyverse)
library(cowplot)
library(EnhancedVolcano)
library(biomaRt)
library(AnnotationDbi)
library(tidyverse)
library(GO.db)
library(org.Mm.eg.db)
library(org.Hs.eg.db)
library(clusterProfiler)
library(DESeq2)
library(EnhancedVolcano)

Project Setup

1. Create a new project called omicsAD.
   • Click the File menu button, then New Project.
   • Click New Directory.
   • Click New Project.
   • Type omicsAD as the directory name. Create the project anywhere you like, but don’t forget where you put it!
   • Click the Create Project button. This will create a file called omicsAD.Rproj in the directory you just created. In the future you can double-click on this file to open RStudio in this directory. This will be the easiest way to interact with the files/code you produce in this workshop.
2. Use the Files tab to create a data folder to hold the data, a scripts folder to house your scripts, a results folder to hold results, and a doc folder to hold project-related documents. Alternatively, you can copy and paste the following commands into the R console for step 2 only. You still need to create a project with step 1.

dir.create("data")
dir.create("scripts")
dir.create("results")
dir.create("doc")