This repo contains the course material for NBIS workshop Single Cell RNA-Seq Data Analyses. The rendered view of this repo is available here.
# for seurat and bioconductor labs
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq-seurat:20250320-2311`
# for scanpy labs
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq-scanpy:20250325-2256
# for optional spatial labs
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq:2024-seurat_spatial-r4.3.0
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq:2024-bioconductor_spatial-r4.3.0
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq:2024-scanpy_spatial-py3.10
-
Create a new directory and
cdinto it. You will mount this directory to/home/jovyan/workin your container so that you can save your work locally. -
To run Seurat or Bioconductor labs in RStudio
docker run --rm --platform=linux/amd64 -p 8787:8787 -v ${PWD}:/home/jovyan/work ghcr.io/nbisweden/workshop-scrnaseq-seurat:20250320-2311
Open in browser: http://localhost:8787/
- To run Python labs in JupyterLab
docker run --rm --platform=linux/amd64 -p 8888:8888 -v ${PWD}:/home/jovyan/work/work ghcr.io/nbisweden/workshop-scrnaseq-scanpy:20250325-2256
Open in browser: http://localhost:8888/lab and use password scrnaseq
- In the container, start a terminal and run the command below to activate the respective conda environment.
# for seurat/bioconductor
conda activate seurat
# for scanpy
conda activate scanpy
- To download the compiled labs for the respective toolkit, run the
download-labs.shcommand below provided in the container.
# for seurat
~/download-labs.sh "https://github.com/NBISweden" "workshop-scRNAseq" "compiled/labs" "seurat" "work/labs"
# for bioconductor
~/download-labs.sh "https://github.com/NBISweden" "workshop-scRNAseq" "compiled/labs" "bioc" "work/labs"
# for scanpy
~/work/download-labs.sh "https://github.com/NBISweden" "workshop-scRNAseq" "compiled/labs" "scanpy" "work/labs"
2025 • NBIS • SciLifeLab
