2 Set up

For this workshop you will have available a VM. However, if you which to use your local computer here are the set up instructions:

IMPORTANT: If you have an M1 Mac - Make sure you have gfortan.

2.1 Get the workshop material and data

In RStudio create a new project. This ensures all the files for this workshop are placed in their own folder.

Once you’ve created a new project, run the following R code

2.2 Package Installation

For this workshop, several packages need to be installed.

BiocManager likes to update installed packages, but we have disabled this in the R code below. If your installation fails, then you might need to turn updates on. Note that if there are a large number of packages that BiocManager wants to update it can take several hours.

These instructions have been tested with R version 4.2.1 and Bioconductor version 3.16.

## Install required packages for Seurat:
install.packages(c("Seurat", "dplyr", "remotes", "R.utils","harmony"))

## Install required Bioconductor packages
install.packages("BiocManager")
BiocManager::install(c('SingleR', 'celldex',
                       'BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
                       'limma', 'S4Vectors', 'SingleCellExperiment',
                       'SummarizedExperiment','edgeR' ),
                     update=FALSE)


## install clustree
install.packages("clustree")
install.packages("RColorBrewer")

2.3 Raw Data

# where are you? what folder are you working in

getwd()
#> [1] "/Users/lper0012/Dropbox/BioPlatform/Teaching/Nov2023_scRNAseq_workshop"

## Download and untar the data
options(timeout=3600)
download.file(
    "https://bioinformatics.erc.monash.edu/home/lper0012/SingleCellWorkshopData/data.tar","data.tar")

untar("data.tar")