workshop-scRNAseq

This repo contains the course material for NBIS workshop Single Cell RNA-Seq Data Analyses. The rendered view of this repo is available here.

Environment

# 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:20260323-2301

Run labs interactively (locally)

To run the labs locally follow these instructions to install Docker Desktop / Colima, depending on your operating system.

IMPORTANT: If you are using an Apple Silicon (M-chip) you need to follow the Colima instructions!

• Create a new directory and cd into it. You will mount this directory to /home/jovyan/work in 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 ghcr.io/nbisweden/workshop-scrnaseq-scanpy:20260323-2301

# Apple Silicon with Colima
docker run --rm --platform=linux/amd64 -p 8888:8888 -v scanpy-labs:/home/jovyan/work ghcr.io/nbisweden/workshop-scrnaseq-scanpy:20260323-2301

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 environment.

# for seurat/bioconductor
conda activate seurat

For Scanpy we are using Pixi as environment manager and you do not need to activate the environment. If you are running a command from /home/jovyan you just need to prepend any command with pixi run <CMD>. In any other directory, you need to tell Pixi which manifest to use as shown below.

pixi run --frozen --manifest-path /home/jovyan/pixi.toml <CMD>

• To download the compiled labs for the respective toolkit, run the download-labs.sh command 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
~/download-labs.sh "https://github.com/NBISweden" "workshop-scRNAseq" "compiled/labs" "scanpy" "work/labs"

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2026 • NBIS • SciLifeLab