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
1.1. 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.
1.2. 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.
1.3. 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.
1.4. 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
1.5. 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.
1.6. 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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.
Natural language support but running in an English locale
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.
>
1.7. Following the workshop, you can remove R and RStudio. As an Admin user, go Start > Settings > Apps & Features. Click on the program to remove and click Uninstall.
1.1. RStudio depends on the R programming environment, so we have to install that first. In a web browser, open: https://cran.rstudio.com/bin/macosx. - Note that newer Macs will use Silicon build, older Macs (pre 2020) will use Intel builds. (You can confirm your architecture under About this Mac: Chip; “Apple M” indicates Silicon. ) - Right-click to download the latest version (e.g. “R-4.4.2”“, though the specific version may be slightly different). - Open the downloaded executable to launch the R installer.
1.2. 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.
1.3. To install RStudio, in a web-browser, open: - https://rstudio.com/products/rstudio/download/#download and click on Download RStudio Desktop for Mac.
1.4. 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.
1.5. 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.
1.6. 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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.
Natural language support but running in an English locale
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.
>
1.7. Following the workshop, you can remove R and RStudio. Open your Applications directory, and drag the R and RStudio application into the Trash.
A few R libraries depend on external software programs.
2.1 Install the Miniconda package manager as detailed here
2.2 Open a command/teminal window and create and activate a new Conda environment
conda create -n isc
conda activate isc2.3 Install required software using Conda:
# Required by BPCells
conda install -y conda-forge::hdf5
# Optional: used by Leiden clustering algorithm
conda install -y conda-forge::leidenalg
# Optional: used to convert Illumina BCLs to FASTQs
conda install -y bioconda::bcl2fastq-nextseq
2.4 Optional: Install Cell Ranger (Useful only if you have to rerun Cell Ranger on data you received from a sequencing facility.) See detailed installation instructions at 10x Genomics
3.1 The workshop exercises requires the installation of special R packages. To install them into RStudio:
- one at a time, copy the blocks of code below and paste into the RStudio
**Console** tab
- make sure the block you just pasted is highlighted and press **Enter**
to execute.
- as the installation progresses, you might see red text flash by
and that's ok (typically an informative blurb or minor warning that has
no downstream impact).
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")
# Allows data to live on disk instead of in RAM
# https://github.com/bnprks/BPCells
remotes::install_github("bnprks/BPCells/r")
# Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
# https://github.com/ZJUFanLab/scCATCH
install.packages("scCATCH")
# -----------------------------------------------------------------------------
# OPTIONAL libraries
# Some of the libraries make the code execute faster and some enable some off-menu options (e.g. Leiden clustering)
# The workshop notes will work fine without these libraries below but may be slower.
# -----------------------------------------------------------------------------
# Presto makes it fast and easy to run Wilcoxon rank sum test and auROC analysis on large datasets
# https://github.com/immunogenomics/presto
devtools::install_github("immunogenomics/presto")
# Accelerates DESeq2 diffex analysis by fiting Gamma-Poisson Generalized Linear Models Reliably
# https://github.com/const-ae/glmGamPoi
BiocManager::install("glmGamPoi")
# An alternative to Louvain clustering algorithm
# https://cran.r-project.org/package=leiden ; https://github.com/TomKellyGenetics/leiden
install.packages("leiden")3.2 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.
3.3. 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.
3.4. If you don’t see the above warning, and the output ends like below then you the libraries were successfully installed:
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$Version3.5. Press Control-Q close RStudio; when prompted to Save workspace image…, click Don’t Save.