R and RStudio
To install R and RStudio, you must have administrator privileges on your machine. Choose the version appropriate for your operating system. You can also watch a video for a Mac or a Windows install (you only need to install R and RStudio, and none of the other programs mentioned in the videos). Please also note that the versions of R and RStudio in the video are older. Instead, install or update to the latest version supported by your operating system.
Install R
-
Choose among “Download and Install R” section (not “Source Code for all Platforms”).
Latest version: 4.1.2
(only for macOS Yosemite or older: legacy version 3.3.3)
Note for Mac users
If you have an M1 (and higher) Mac, you must install the Intel version of R (Bioconductor packages installed below are not yet compatible with the arm64 version).
Note for all users
You must have R installed before proceeding to the next step.
Install RStudio
Go to https://rstudio.com/products/rstudio/download/#download
Select the FREE Desktop version.
-
Choose among “Installers for Supported Platforms” section (not “Zip/Tarballs”) or follow the link to older versions of RStudio if you need a legacy version.
Latest version: 2021.09.0
(only for macOS El Capitan and older: legacy version 1.1.463)
Install R packages
Open RStudio, then:
- Select the “Console” tab of the left panel
.
-
Copy the following code after the prompt
>
to install all necessary packages:
if (!require(tidyverse)) install.packages("tidyverse") if (!require(pheatmap)) install.packages("pheatmap") if (!require(RColorBrewer)) install.packages("RColorBrewer") if (!require(BiocManager)) install.packages("BiocManager") if (!require(DESeq2)) BiocManager::install("DESeq2") if (!require(plyranges)) BiocManager::install("plyranges")
While installing (or updating, see below) packages, you might be prompted:
There is a binary version available, but the source version is later: <table of package names> Do you want to install from sources the package which need compilation? (Yes/no/cancel)
Always enter
no
followed by enter. -
Update packages by selecting the “Packages” tab of the bottom right panel
and then click on “Update”
.
-
If any packages are listed, first click on “Select All”
and then “Install Updates”
.
Check that it worked
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Troubleshooting
RStudio looks incorrect
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If you confirmed RStudio is open but don’t see the same panels as depicted above, then in the RStudio menu bar, select View > Panes > Show all panes.