The steps below are oriented toward advanced users who would like to install and configure select software on their local workstation. These steps are not necessary or recommended, but may provide context for advanced use-cases.
These instructions build on the install detailed in the basic setup instructions; please see that document for more details on setting up Zoom, Slack, and also for getting help.
Note that if you do not have Administrative privileges it will be tricky to install R/RStudio; you may need to coordinate with your System Admin/IT Support team to get these installed.
Note that these instructions are focused on R/RStudio and dependent libraries (e.g. Seurat). Seperate instructions on downloading and installing Cell Ranger can be found here: https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-in
RStudio depends on the R programming environment, so we have to install that first. In a web browser, open: https://cran.rstudio.com/bin/windows/base/ and click “Download R 4.3.2 for Windows” (the version may be slightly different). Open the downloaded executable to launch the R installer.
The installer will walk through several options; accept all the defaults (by repeatedly clicking Next) and when prompted, click Install. The installer will show a progress bar; the process takes about 2 minutes; click Finish when prompted to close the installer.
To install RStudio, in a web-browser, open: https://rstudio.com/products/rstudio/download/#download and click on Download RStudio Desktop for Windows. Open the downloaded executable to launch the installer.
The installer will either prompt you to login as an Admin user or (if your current account has Admin privileges) simply ask you to allow it to make changes. Click Yes
The installer will walk through several options; accept all the defaults (by repeatedly clicking Next) and when prompted, click Install. The installer will show a progress bar; the process takes less than one minute; click Finish when prompted to close the installer.
Press Windows+R keys to open the Run dialog; type “RStudio” in the text box and hit enter. This will launch a new RStudio window. The RStudio window is divided into several panes. The lower left pane shows the Console tab and will show some text followed by a command prompt (>):
R version 4.3.2 (2023-10-31) – “Eye Holes” Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type ‘license()’ or ‘licence()’ for distribution details.
R is a collaborative project with many contributors. Type ‘contributors()’ for more information and ‘citation()’ on how to cite R or R packages in publications.
Type ‘demo()’ for some demos, ‘help()’ for on-line help, or ‘help.start()’ for an HTML browser interface to help. Type ‘q()’ to quit R.
The workshop exercises requires the installation of special R libraries. To install them into RStudio:
if (!requireNamespace(\"BiocManager\", quietly = TRUE)) {\
install.packages(\"BiocManager\")\
requireNamespace(\"BiocManager\", quietly = TRUE)
}
install.packages("devtools")
install.packages("remotes")remotes::install_github("satijalab/seurat", "seurat5")
remotes::install_github("satijalab/seurat-data", "seurat5")
remotes::install_github("satijalab/seurat-wrappers", "seurat5")devtools::install_github("immunogenomics/presto")
BiocManager::install("glmGamPoi")Note: These installations automatically trigger the installation of a litany of dependent libraries so you will see repeated progress bars and code flying by in the Console window. The large set of dependencies mean that if you are installing from scratch it can take several hours. So now is a good time to make some coffee/tea (or a loaf of bread) while RStudio cooks.
If there was a problem during the installation, R will display a block like this:
Warning in install.packages: Installation of package ‘xxx’ has non-zero exit status.
If this comes up, you will need to troubleshoot the install based on the error or the specific package that failed.
The downloaded binary packages are in C:\Users\some\path\Temp\downloaded_packages
You can check this with the following code block:
# Quietly load Seurat and print the version
# It should be version 5 or later
suppressPackageStartupMessages(library(Seurat))
sessionInfo()$otherPkgs$Seurat$Versionhttps://cran.rstudio.com/bin/macosx/
and click the link “R-4.3.2.pkg” (the version may be slightly different). Open the downloaded executable to launch the R installer.
The installer will walk through several options; accept all the defaults (by repeatedly clicking Continue) and when prompted, click Install. The installer will prompt you to confirm your username/password. The installer will show a progress bar; the process takes about 1 minutes; click Finish when prompted to close the installer.
To install RStudio, in a web-browser, open:
Opening the downloaded executable opens a window with “RStudio” and your Applications folder icons. Drag the RStudio into the Applications folder. (If you see a dialog that claims RStudio already exists, click Keep Both.) The installer will prompt you to confirm your username/password.
The installer will walk through several options; accept all the defaults (by repeatedly clicking Next) and when prompted, click Install. The installer will show a progress bar; the process takes less than one minute.
When completed, open the Applications folder and double-click on the RStudio application. You will see a dialog “RStudio.app is an app downloaded from Internet. Are you sure you want to open it?” Click Open. This will launch a new RStudio window. The RStudio window is divided into several panes. The lower left pane shows the Console tab and will show some text followed by a command prompt (>):
R version 4.3.2 (2023-10-31) – “Eye Holes” Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type ‘license()’ or ‘licence()’ for distribution details.
R is a collaborative project with many contributors. Type ‘contributors()’ for more information and ‘citation()’ on how to cite R or R packages in publications.
Type ‘demo()’ for some demos, ‘help()’ for on-line help, or ‘help.start()’ for an HTML browser interface to help. Type ‘q()’ to quit R.
The workshop exercises requires the installation of special R libraries. To install them into RStudio:
if (!requireNamespace(\"BiocManager\", quietly = TRUE)) {\
install.packages(\"BiocManager\")\
requireNamespace(\"BiocManager\", quietly = TRUE)
}
install.packages("devtools")
install.packages("remotes")remotes::install_github("satijalab/seurat", "seurat5")
remotes::install_github("satijalab/seurat-data", "seurat5")
remotes::install_github("satijalab/seurat-wrappers", "seurat5")devtools::install_github("immunogenomics/presto")
BiocManager::install("glmGamPoi")Note: These installations automatically trigger the installation of a litany of dependent libraries so you will see repeated progress bars and code flying by in the Console window. The large set of dependencies mean that if you are installing from scratch it can take several hours. So now is a good time to make some coffee/tea (or a loaf of bread) while RStudio cooks.
If there was a problem during the installation, R will display a block like this:
Warning in install.packages: Installation of package ‘xxx’ has non-zero exit status.
If this comes up, you will need to troubleshoot the install based on the error or the specific package that failed.
The downloaded binary packages are in C:\Users\some\path\Temp\downloaded_packages
You can check this with the following code block:
# Quietly load Seurat and print the version
# It should be version 5 or later
suppressPackageStartupMessages(library(Seurat))
sessionInfo()$otherPkgs$Seurat$Version