docker-scanpy

Docker container for single-cell transcriptomics analysis

• Framework: scanpy
• Doublet detection: scrublet
• Celltyping: celltypist
• Integration: bbknn, harmonypy, pyliger, scvi, scanorama, scib-metrics
• Utils: distinctipy, pickle, pooch
• Other: jupyterlab, quarto, vscode

Run container

## to run jupyterlab
docker run --rm --platform=linux/amd64 -p 8888:8888 -v ${PWD}:/home/jovyan/workdir ghcr.io/royfrancis/scanpy:latest

## to run python commands
docker run --rm --platform=linux/amd64 -u 1000:1000 -v ${PWD}:/home/jovyan/workdir ghcr.io/royfrancis/scanpy:latest python --version

Build container

docker build --platform=linux/amd64 -t scanpy:latest --file dockerfile .

Versions

v1.3

• Updated quarto to 1.7.32
• Added distinctipy for distinct colors
• Added pip-review
• Added pyliger
• Added pooch

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2025 Roy Francis