1. For the single cell section, we will be using Conda for managing and installing the necessary software. please follow the instructions depicted here on how to install and use conda environments: conda instructions. PS.: As mentioned in the instructions, Windows users are required to proceed with the Linus subsystem or via VirtualBox.

2. After installation of conda you can use one of the following files to create your environemnt for the course:

• For MacOS: environment_macos.yml
• For Linux/Windows: environment_linux.yml

The only difference between the environments is the list of compiler packages that are specific for each operationsl system. After sucessful creation of the environment following the conda instructions, you will be able to use 'Rstudio' with 'R 3.6.1' and 'Seurat 3.2.0' and several other associated packages.

3. Additionaly, but optional, installation of other packages not compatible via CONDA can be done within the environment via standard R packages already included in the environment ('devtools', 'install.packages' and 'BiocManager'). Some packages of notice are:

devtools::install_github('satijalab/seurat-wrappers')
devtools::install_github("immunogenomics/harmony")
BiocManager::install("batchelor")
BiocManager::install("glmpca")
BiocManager::install("tradeSeq")

On MacOS, you might need to do this before starting rstudio:

CONDA_BUILD_SYSROOT='/opt/MacOSX10.9.sdk'
# or
CONDA_BUILD_SYSROOT='/Library/Developer/CommandLineTools/SDKs/MacOSX10.9.sdk'

On Ubuntu, you might need to do this AFTER starting rstudio. The Seurat package will fail

install.packages('stringi')
library(Seurat)

• Pre-course instructions