Skip to content

NBISweden/workshop-scRNAseq

Repository files navigation

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.

Contributing

To add or update contents of this repo (for collaborators), first clone the repo, create a new branch, make changes/updates as needed, stage the changes, commit it and push the new branch to GitHub. Then, on GitHub, send a pull request to master.

git clone --depth 1 --single-branch --branch master https://github.com/nbisweden/workshop-scrnaseq.git
git checkout -b <branch-name>
git add .
git commit -m "I did this and that"
git push -u origin <branch_name>

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: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

Run labs interactively (locally)

  • 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/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.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
~/work/download-labs.sh "https://github.com/NBISweden" "workshop-scRNAseq" "compiled/labs" "scanpy" "work/labs"

Render labs

Instructions to render the .qmd files to .html.

  • For Seurat labs
# r/seurat
docker run --rm -ti --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work ghcr.io/nbisweden/workshop-scrnaseq-seurat:20250320-2311 quarto render /work/labs/seurat/seurat_01_qc.qmd

# r/bioc
docker run --rm -ti --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work ghcr.io/nbisweden/workshop-scrnaseq-seurat:20250320-2311 quarto render /work/labs/bioc/bioc_01_qc.qmd

# python/scanpy
docker run --rm -ti --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/work ghcr.io/nbisweden/workshop-scrnaseq-scanpy:20250325-2256 quarto render /work/labs/scanpy/scanpy_01_qc.qmd
  • Successfully rendered outputs are moved to docs folder and chunks are cached under _freeze.

Scripts

To render all qmd files in the repo to docs/ as html output, run

bash scripts/render.sh all

The render.sh script has options to render all of the docs/scripts that are needed, but also to render different parts. The options are:

  • all - run all the steps
  • seurat - render all seurat labs
  • bioc - render all bioc labs
  • scanpy - render all scanpy labs
  • spatial - render all 3 spatial labs.
  • site - render all site stuff like lectures, contents, schedule etc.
  • compile - compile labs into Rmd/ipynb

To compile all qmds into compiled/labs as qmds and ipynb with evaluated meta variables, can also be run directly with the compile script using:

bash scripts/compile.sh

2025 • NBIS • SciLifeLab

About

Single cell RNA sequencing analysis course

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

 
 
 

Contributors 4

  •  
  •  
  •  
  •