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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 labs
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq:2024-seurat-r4.3.0
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq:2024-seurat_spatial-r4.3.0

# for bioconductor labs
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq:2024-bioconductor-r4.3.0
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq:2024-bioconductor_spatial-r4.3.0

# for python labs
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq:2024-scanpy-py3.10
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-scrnaseq:2024-scanpy_spatial-py3.10

Run labs interactively (locally)

  • Launch docker container in the project's root folder
  • To run Seurat or Bioconductor labs in RStudio
docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/home/rstudio/workdir ghcr.io/nbisweden/workshop-scrnaseq:2024-seurat-r4.3.0
docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v ${PWD}:/home/rstudio/workdir ghcr.io/nbisweden/workshop-scrnaseq:2024-bioconductor-r4.3.0

  • Open in browser: http://localhost:8787/, login: rstudio, pass: scrnaseq

  • Navigate to /home/rstudio/workdir/labs and open qmd files

  • To run Python labs in JupyterLab

docker run --rm -ti --platform=linux/amd64 -p 8888:8888 -v ${PWD}:/home/jovyan/workdir ghcr.io/nbisweden/workshop-scrnaseq:2024-scanpy-py3.10
  • Open in browser: http://127.0.0.1:8888/lab?token=xxxx (Use exact token from terminal on launch)
  • Navigate to /home/jovyan/workdir/compiled/scanpy and open .ipynb files

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:2024-seurat-r4.3.0 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:2024-bioconductor-r4.3.0 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:2024-scanpy-py3.10 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

To compile all qmds into compiled/labs as qmds and ipynb with evaluated meta variables, run

bash scripts/compile.sh

2024 • NBIS • SciLifeLab