Claude Code — AI Coding Agent for Your Repo
Claude Code is a coding agent that reads your project, edits files, and runs commands under your approval. Powerful on …
Reproducibility
Snakemake — Reproducible Analysis Pipelines in Python
Snakemake declares rules with inputs and outputs, reruns only what changed, and scales from laptop to cluster unchanged. …
uv — Fast Python Environments With Lockfiles
uv replaces pip, venv, and pyenv with one fast binary and a lockfile by default. The best way to start a Python project …
Conda — Environments for Scientific Python and Beyond
Conda installs the binary dependencies pip cannot — CUDA, GDAL, compilers, R. Heavier and slower than uv, and still the …
Apptainer — Containers That HPC Clusters Allow
Apptainer runs containers without root, which is why university clusters permit it and ban Docker. Single-file images …
Docker — Containers for Reproducible Research
Docker packages your entire computational environment into an image that runs identically anywhere. The strongest …
Quarto — Reproducible Documents From One Source
Quarto renders Markdown with executable R and Python chunks to PDF, Word, HTML, or slides. Your figures regenerate from …
Code Automation
Git and GitHub for Researchers: Version Control Your Work Without Fear
A complete guide to using Git and GitHub for research code, data scripts, and even your thesis — explained for …
GitHub — Version Control and Sharing for Research Code
GitHub gives research code a full history, a citable DOI through Zenodo, and a home reviewers can reach. Free, and the …