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.
git clone --depth 1 --single-branch --branch master https://github.com/nbisweden/workshop-scrnaseq.git
Make changes/updates as needed. Add the changed files. Commit it. Then push the repo back.
git add .
git commit -m "I did this and that"
git push origin
Environment
# for seurat labs
docker pull susrei/workshop-scrnaseq:2023-seurat-r4.3.0-conda-231204
# for bioconductor labs
docker pull susrei/workshop-scrnaseq:2023-bioconductor-r4.3.0-conda-231204
# for python labs
docker pull susrei/workshop-scrnaseq:2023-scanpy-py3.10
Run labs
-
Launch docker container in root of the repo
-
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 susrei/workshop-scrnaseq:2023-seurat-r4.3.0-conda-231204
docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir susrei/workshop-scrnaseq:2023-bioconductor-r4.3.0-conda-231204
-
Open in browser:
http://localhost:8787/, login: rstudio, pass: scrnaseq -
Navigate to
/home/rstudio/workdir/labsand open qmd files -
To run Python labs in Jupyter notebook
docker run --rm -ti --platform=linux/amd64 -p 8888:8888 -v $PWD:/home/jovyan/workdir susrei/workshop-scrnaseq:2023-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/scanpyand open .ipynb files
Render
Instructions to render the .qmd files to .html.
- For Seurat labs
docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir susrei/workshop-scrnaseq:2023-seurat-r4.3.0-conda-231204 quarto render /home/rstudio/workdir/labs/seurat/seurat_01_qc.qmd
- For Bioconductor labs
docker run --rm -ti --platform=linux/amd64 -p 8787:8787 -e PASSWORD=scrnaseq -v $PWD:/home/rstudio/workdir susrei/workshop-scrnaseq:2023-bioconductor-r4.3.0-conda-231204 quarto render /home/rstudio/workdir/labs/bioc/bioc_01_qc.qmd
- For Python labs
docker run --rm -ti --platform=linux/amd64 -p 8888:8888 -v $PWD:/home/jovyan/workdir susrei/workshop-scrnaseq:2023-scanpy-py3.10 quarto render /home/jovyan/workdir/labs/scanpy/scanpy_01_qc.qmd
- Successfully rendered outputs are moved to
docsfolder and chunks are cached under_freeze.
2024 โข NBIS โข SciLifeLab