Docker container extending Bioconductor Docker for HPC (Apollo/Gemini) and VSCode devcontainer workflows.
| Guide | Audience | Content |
|---|---|---|
| User Guide | End users | JupyterLab, pixi, available packages, how-to guides |
| Developer Guide | Maintainers | Building, upgrading Bioconductor, adding packages |
| Changelog | Everyone | Version history and changes |
- R 4.5 with ~1500 Bioconductor/CRAN packages (Seurat, DESeq2, etc.)
- Python 3.12 with SCverse ecosystem (scanpy, scvi-tools, etc.)
- GNU Octave (free MATLAB alternative)
- SoS polyglot notebooks (mix R, Python, Bash in one notebook)
Pre-configured with productivity extensions:
- Code intelligence (LSP), formatting (black), spellchecker
- Execution time, resource monitor, git integration
- Dev server proxying (Shiny, Streamlit, Gradio)
- pixi - Fast conda alternative for installing additional packages
- Genomics - bcftools, samtools, bedtools, sra-tools
- VS Code CLI - serve-web and tunnel support
- Install Dev Containers extension
- Open repo in VSCode → "Reopen in Container"
~/bin/ij 4 # Request 4 CPUsdocker run -it --rm ghcr.io/drejom/vscode-rbioc:latest /bin/bashContainer (lean, ~2-3GB) Shared Libraries (HPC storage)
┌─────────────────────────┐ ┌─────────────────────────────┐
│ System deps, tools │ │ rlibs/bioc-3.22/ (R) │
│ JupyterLab + extensions │──────▶│ python/bioc-3.22/ (Python) │
│ pixi, VS Code CLI │ │ Shared by all users │
└─────────────────────────┘ └─────────────────────────────┘
| Tag | Example | Use Case |
|---|---|---|
latest |
:latest |
Most recent build |
RELEASE_X_YY |
:RELEASE_3_22 |
Specific Bioconductor version |
vX.Y.Z |
:v3.22.0 |
Stable release |
vYYYY-M-DD |
:v2026-1-8 |
Dev release |
MIT