quadbio Claude Code plugins

A Claude Code plugin marketplace for quadbio's plugins.

Plugin	What it does
analysis-workflow	Conventions, guard hooks and a small package for analysis repos where humans (notebooks) and coding agents (scripts) work side by side.
cell-type-annotation	Evidence-driven cell-type annotation of pre-clustered single-cell and spatial data.
euler-hpc	Run coding agents on ETH Zurich's Euler cluster: node, allocation, storage rules and your setup at session start; skills for Slurm jobs, software and data; jobs listed by session.
research-agent-skills	How agents write research code, run and hand over research tasks, and set up a project so Claude Code and Codex read the same instructions.
sci-figures	Nature-style research figures and their legends, with a small matplotlib package for style, layout and export.

Install once per machine; each plugin's README says how to use it.

claude plugin marketplace add quadbio/claude-plugins
claude plugin install <plugin>@quadbio

Then turn on updates, which are off by default for marketplaces outside Anthropic's: in a session, /plugin → Marketplaces → quadbio → Enable auto-update (docs).

Auto-update runs when Claude Code starts. To update by hand, refresh the marketplace, then the plugin; the new version applies from the next session:

claude plugin marketplace update quadbio
claude plugin update <plugin>@quadbio

A plugin option's default applies only once the option is saved, and an update doesn't ask for the options it adds: set them in /plugin → the plugin → Configure options.

Conventions

The plugins here form a growing, modular ecosystem that allows for alternative working styles while minimizing duplication and friction. A new plugin, and every change to one, follows these rules; anything they don't cover is the plugin's own choice.

Modular.

• Each rule has one home. A plugin that builds on another defers to it instead of restating its rules, as cell-type-annotation does for analysis-workflow. If it needs the other to work, it lists it under dependencies in its plugin.json, so installing it installs the other, and its Develop section says to load both.
• Depending on a plugin whose other parts you don't use is fine. If those parts would contradict yours, agree with its maintainers how to separate what you need, rather than copying it.
• Skills are cut so that a request loads what it needs and little else; the skills of one plugin don't overlap.

Alternatives. A plugin may do another plugin's job in a different way, such as an alternative to euler-hpc. It replaces that one plugin and builds on the rest like any other. Its README names the plugin it replaces, how it differs and whether both work installed together, so users can choose.

Little always-on context. Rules go in skills, which load on demand. Hooks are for what must hold in every session, and print little at session start: every installed plugin's output lands in every session.

One project layout, so plugins agree on it:

• a repo's agent instructions live in one AGENTS.md, which Codex reads, and a CLAUDE.md imports it (@AGENTS.md) for Claude Code, which skips AGENTS.md when a CLAUDE.local.md or a parent folder's CLAUDE.md exists;
• worktrees live in .claude/worktrees/, where claude --worktree creates them, and .gitignore lists that folder.

Repository. Each plugin lives in its own quadbio repository; this one only lists them.

• Its README opens with what it does and its parts, then Use, Install (pointing here), Develop, Release.
• claude plugin validate . passes.
• Values that differ between people or labs (paths, groups, hardware) are userConfig options, not hard-coded. Hooks and skills get only saved values, never the default, so each works when an option is missing.
• Repositories are public: no absolute paths, usernames, hostnames, private repository names or infrastructure details.

Release. Entries follow each plugin's main: a plugin releases by bumping version in its plugin.json.

Contributing. Fixes and changes to a plugin's existing parts go straight to a pull request. For a new part, first agree with its maintainers in an issue where it goes; another way of doing its job, or work released on its own schedule, is a plugin of its own. To add a plugin, open a pull request here that adds its entry to .claude-plugin/marketplace.json and its row above.