Single Cell RNAseq Workshop

Workshop materials for scRNAseq Analysis in R with Seurat, run by members of QCIF, SIH, Monash, and the Australian BioCommons. Topics covered include QC, normalisation, dimensionality reduction, batch correction (Harmony), clustering, cell type annotation (SingleR), and differential expression.

Visit the Workshop page.

Repository structure

Path	Description
part1/ and part2/	Workshop sections (*.Rmd files) that learners work through sequentially with follow-along and self-guided exercises
data/	Input datasets used during the workshop
scripts/	Helper and preprocessing scripts
setup/	Training environment (VM) setup files
_bookdown.yml, _output.yml, _common.R, etc.	Auxiliary files for rendering the bookdown site

Environment setup

1. Install CRAN, bioconductor, and github packages:

bash setup/setup.sh install_packages

Review any failed package installs and resolve manually in an interactive R session. Usually due to missing dependencies in the output log.

2. Move relevant files and folder structure for the VM:

bash setup/setup.sh prep_data

3. Remove unneeded files and folders:

bash setup/setup.sh clean

4. Start up the rstudio server:

module load rstudio
sudo rstudio-server start

5. Open rstudio in the browser with the url provided from rstudio-server start.