Research Skills

Cross-agent marketplace for academic research workflows and development tooling. Install individual plugins for literature search, grant proposals, manuscript preparation, figures, presentations, project lifecycle management, and neuroinformatics.

[!TIP]
This marketplace is taught week-by-week in the free Agentic Research Course from the Open Science Collective.

Install

Claude Code

In Claude Code, type /plugin, select Add marketplace, enter:

neuromechanist/research-skills

Then select which plugins to install. Each plugin is independent.

Install all plugins via CLI:

claude plugin marketplace add neuromechanist/research-skills
for p in project grant manuscript opencite figures presentation neuroinformatics; do
  claude plugin install "$p@research-skills"
done

Codex

Codex can use the native repo marketplace at .agents/plugins/marketplace.json; the Claude-compatible .claude-plugin/marketplace.json remains for legacy-compatible installs.

codex plugin marketplace add neuromechanist/research-skills
codex plugin marketplace add ./path/to/research-skills

Each plugin also has a native .codex-plugin/plugin.json manifest. Then open /plugins in Codex and install the plugins you need.

GitHub Copilot CLI

Copilot CLI can use the native marketplace at .github/plugin/marketplace.json. Each plugin also has a native .github/plugin/plugin.json manifest.

copilot plugin marketplace add neuromechanist/research-skills
copilot plugin marketplace browse research-skills
copilot plugin install project@research-skills

See docs/cross-agent-compatibility.md for the researched registration paths and source links.

Plugins

Skills auto-trigger on user intent (described per-plugin below). Slash commands are reserved for workflows that need explicit orchestration entry points.

Research Plugins

opencite

Search academic literature, explore citation graphs, download PDFs, and export BibTeX. Wraps the opencite CLI, aggregating Semantic Scholar, OpenAlex, PubMed, arXiv, and bioRxiv.

"Find the top 10 most cited papers on brain-computer interfaces"
"Look up DOI 10.1038/nature12373 and download the PDF"
"Convert this PDF to markdown"

grant

Draft and review NIH and NSF grant proposals with mechanism-specific templates (R01, R21, K99, CAREER, etc.). Includes a grant-figure-qa skill that checks figures for resolution, accessibility, and NIH/NSF compliance. As of epic #61, grant-review and grant-figure-qa use thin-dispatch skills with Claude-bundled fresh-context agents, Codex agent templates, and Copilot plugin-agent templates; when those agents are not configured, the skills run the same reference procedure inline. Skills for research strategy guidelines, writing style, budget justification, scoring criteria, and resubmission response.

"Write the significance section for an R01 on motor cortex"
"Review my R21 proposal at proposal.pdf as an NIH study section"

manuscript

Academic manuscript toolkit covering the full lifecycle: literature review (both multi-phase citation-traceable corpus protocol and single-pass thematic synthesis), writing guidance (IMRAD structure, section templates), peer review (methodology, statistics, reproducibility), and journal-specific formatting (IEEE, Nature, PNAS, Elsevier, LaTeX/BibTeX management). Includes revision response templates. As of epic #61, paper-review is a thin-dispatch skill with a Claude-bundled fresh-context agent, a Codex agent template, and a Copilot plugin-agent template; when those agents are not configured, the skill runs the same reference procedure inline.

The manuscript:lit-review skill covers two modes: a rigorous, iterable, citation-traceable multi-phase workflow where every claim in a direction paper links back to a paper-card on disk, plus an express single-pass synthesis pipeline for writing an Introduction or Background section. The multi-phase workflow can delegate phase orchestration (epic issue, sub-issues, worktrees, state file) to project:epic-dev for git-tracked reviews.

"Review this manuscript at paper.pdf as a peer reviewer"
"Format my paper for Nature Neuroscience"
"Start a multi-phase lit review on EEG-based BCIs with strands tools, data, science"
"Write a single-pass literature review on motor cortex oscillations"

figures

Publication-quality figures plugin (Nature, Science, PNAS, Cell, and other journals). v0.10.6 fixes ai-full-figure and svg-primitives SKILL frontmatter loadability. v0.10.5 adds native Copilot plugin metadata for the QA agent template. v0.10.4 makes validate_fonts.py viewBox-aware so it reports the physical point size (a bare font-size in an mm-viewBox is mm, not pt), which lets svg-primitives output pass figure-qa's font check, and completes the svg-figure examples migration to svg-primitives (issue #52). v0.10.3 implements the figure-qa SVG-branch geometry section (text-overflow, arrow-tip-to-target, sibling bbox-overlap; issue #47). v0.10.2 makes figure-qa a cross-agent thin-dispatch skill over the existing QA agent (epic #61). v0.10.1 closed epics #31 (plugin redesign) and #48 (svg-primitives): seven skills and the unified QA agent.

• scientific-figure skill — svgutils-based composer that places panels at exact mm coordinates and preserves text as SVG <text> elements so font sizes are inspectable. validate_fonts.py walks the transform stack and folds in the root width/viewBox scale to report the physical point size (a bare font-size in an mm-viewBox is mm, not pt; explicit units are absolute), flagging anything below the journal minimum (Nature 5 pt, Science/Cell/PNAS 6 pt). export.py detects Inkscape on $PATH and uses it when present, falling back to cairosvg. End-to-end example: examples/two-column-figure.py.
• transparent-icons skill — flat scientific icons (brain, neuron, EEG cap, DNA, etc.) via the Codex CLI image_gen tool (preferred when codex login is configured) or the OpenAI Images API (fallback). Transparency post-process: fast Pillow threshold by default or opt-in rembg + BiRefNet for cleaner edges on complex foregrounds. Shares a theme.json schema with the ai-full-figure skill for cross-skill style consistency.
• svg-figure skill — hand-authoring conventions for SVG schematics and the SVG-spec reference for figure-qa. Reference docs cover element-consistency rules, arrow patterns with proper marker geometry, text alignment with bbox arithmetic, and palette compliance (with near-gray exemption for axis chrome). For new Python-driven schematics, prefer svg-primitives instead — svg-figure's SKILL.md leads with that recommendation and each pattern carries a "done automatically by svg-primitives" callout.
• svg-primitives skill — mm-precise SVG builder in Python on drawsvg + svgpathtools + fontTools. Auto-fits text boxes from measured font metrics, snaps arrow endpoints to box edges via path intersection, emits <marker orient='auto'> for tangent-correct arrowheads on straight/cubic/orthogonal/multi-waypoint paths, and uses named layers for deterministic paint order. In-process validation via Canvas.save(validate='warn'|'strict'|'off') and Canvas.validate() runs four checks (text-overflow, arrow-tip-distance, marker-orient, sibling-overlap). Ships LabeledBox, Pill, Diamond, Arrow.connect, Bracket, Annotation, Group, Shape Protocol, and a 68-test E2E suite asserting the invariants on rendered SVGs.
• ai-full-figure skill — AI-generated pictorial substrate via Codex CLI or OpenAI Images API, plus programmatic label / arrow / scale-bar overlay producing a composable SVG. The substrate-only rule keeps the model from hallucinating labels; the overlay step places text deterministically. Hard-ceiling rules route figures that need data plots, equations, multi-arrow flows, or more than ~5 labels back to scientific-figure or svg-primitives. Theme.json bible shared with transparent-icons.
• plot-styling skill — library decision tree across matplotlib, seaborn, plotnine, plotly, and PyVista, with SciencePlots recipes for Nature, IEEE, Science, Cell, PNAS, and APS journals. End-to-end example sciplots_panel.py produces a Nature 1-column panel using science + nature + bright + no-latex that passes the figure-qa plot-script and SVG branches.
• figure-qa skill + agent — a thin dispatch skill (epic #61) that routes to a fresh-context Claude agent when available, with a Codex agent template, a Copilot plugin-agent template, and an inline fallback using the same reference procedure. Type-dispatches across SVG / raster / plot-script / composed-figure inputs. Helper scripts (check_svg.py, check_raster.py, check_plot_script.py) handle programmatic checks (font minima, palette compliance, SVG-branch geometry [text-overflow, arrow-tip-to-target, sibling bbox-overlap], alpha-channel correctness, DPI, library recommendations) with strict separation from VLM rubric scoring (clarity, hierarchy, alignment, palette coherence, journal-fit). Programmatic checks own anything with ground truth; VLM judgment is reserved for "does this look balanced." Complementary to svg-primitives' in-process validators: figure-qa validates arbitrary SVGs (including hand-authored ones); svg-primitives validates SVGs it produced, before they hit disk.

presentation

Create interactive Reveal.js presentations from JSON using the Agentic Presentation Builder. Supports 7 element types (text, bullets, images, Mermaid diagrams, callouts, code blocks, tables), 5 themes, animated progressive reveals, speaker notes, and LaTeX math.

The skill teaches Claude the JSON schema and authoring workflow; the builder repo handles rendering.

"Create a 10-slide academic presentation on EEG signal processing"
"Build a conference talk on brain-computer interfaces"

neuroinformatics

Neuroscience data standards, experiment design, and dataset validation:

• BIDS conversion -- convert EEG, EMG, and other modalities to Brain Imaging Data Structure (BIDS) format with proper file naming, JSON sidecars, and metadata
• Experiment design -- scaffold PsychoPy experiments with stimulus presentation, LSL marker integration, and BIDS-compatible output
• BIDS validator agent -- autonomously validate datasets, diagnose errors, and apply fixes. Claude has the bundled agent shell, Codex has an agent template, and Copilot exposes the .agent.md template through the native plugin manifest.

"Convert ./raw-data to BIDS format, modality EEG, task rest"
"Validate the BIDS dataset at ./bids-dataset"
"Design a visual oddball ERP paradigm with 2 conditions"

Development Plugin

project

Complete project lifecycle toolkit combining initialization, epic/sprint workflow, and CI/CD management:

• init-project -- scaffold new projects with AGENTS.md, a Claude Code CLAUDE.md import wrapper, .rules/, .context/, and config files
• update-rules -- non-destructive sync of AGENTS.md, the CLAUDE.md adapter, and .rules/ against latest templates at user or project level
• epic-dev -- Codex-facing entrypoint for the /epic-dev multi-phase feature workflow with git worktrees, GitHub issues, and phased PR delivery
• workflow-reference -- branch, state-file, worktree, and GitHub command reference for epic/sprint workflows
• pr-review-toolkit -- PR and recent-change review across code quality, tests, error handling, comments/docs, type design, and simplification. Inspired by Anthropic's pr-review-toolkit implementation; the upstream plugin README identifies it as MIT licensed. The project skill is an original cross-agent adaptation with shared rubrics in references/.
• codebase-onboarding -- verified reconnaissance of an unfamiliar codebase or research field before planning or editing: a fixed bootstrap sequence (inventory, intent docs, code, history, what actually runs, SDK probes), parallel read-only explorer fan-out, and a report contract separating verified facts from assumptions
• implementation-planning -- plans a weaker model could execute: two registers by stakes, pre-registered decision gates, load-bearing-claim verification, and a mandatory open-judgment-calls list
• engineering-loop -- the single-PR change workflow: mirror an existing pattern, pin test first for refactors, per-commit gates against a measured baseline, review with all findings addressed or rejected with reasons, plus a detached background-jobs protocol for long-running work
• debugging -- reproduce-isolate-prove-fix-verify with anti-shortcut gates (never weaken tests or guardrails, no silent fallbacks) and a numerical-debugging reference for reference-implementation parity work
• agent-fanout -- orchestrating subagents and teammates: basic spawning/messaging mechanics per tool, role taxonomy with worker-tier model routing, full-lifecycle briefing templates, supervision and synthesis protocols, and a hard cap of 40 agents per run computed before launch
• CI scaffolding -- generate GitHub Actions workflows for Python (ruff + pytest) or TypeScript (biome + bun test)
• Docker packaging -- multi-stage Dockerfiles with uv/bun, health checks, and security hardening
• Security audit -- credential scanning, dependency audit, OWASP checklist, configuration hardening
• Document processing -- PDF/image OCR, text extraction, markdown conversion

Includes autonomous agents: dependency-auditor (vulnerability scanning), release-prep (pre-release validation), and a Claude-bundled pr-review-toolkit reviewer. Codex gets an opt-in TOML agent template under plugins/project/agents/templates/; Copilot exposes the .agent.md template through the native plugin manifest. The skill remains the portable fallback when a fresh-context agent is unavailable.

/init-project "Python EEG analysis package"
/update-rules project
/epic-dev "build a community dashboard"
/release-prep --minor
"Set up CI for this Python project with ruff and pytest"
"Process scanned-document.pdf and convert to markdown"

Structure

research-skills/
├── .claude-plugin/marketplace.json
├── .agents/plugins/marketplace.json
├── .github/plugin/marketplace.json
├── plugins/
│   ├── project/                   # Project lifecycle (init, workflow, CI, Docker, security, docs)
│   ├── grant/                     # Grant proposals (writing, review, figure QA)
│   ├── manuscript/                # Manuscripts (review, writing, formatting)
│   ├── opencite/                  # Literature search and citation management
│   ├── figures/                   # Publication-quality figures + QA
│   ├── presentation/             # Interactive Reveal.js slide decks
│   └── neuroinformatics/          # BIDS, HED, experiment design

Requirements

• Claude Code, Codex, or GitHub Copilot CLI
• For opencite: opencite CLI (uvx opencite)
• For icons: OpenAI API key for the OpenAI Images API, or codex login for the Codex CLI fallback (preferred). The active generate_icon.py uses the latest available OpenAI image model. Optional: rembg + onnxruntime for the BiRefNet transparency post-process (one-time ~400 MB model download).
• For figure composition: svgutils plus an exporter — Inkscape is detected at runtime (brew install inkscape) and cairosvg is the no-system-deps fallback.
• For figure QA: lxml, svgelements, svgpathtools, shapely for the SVG branch; pillow, colorthief for the raster branch; AST analysis for the plot-script branch (no extra deps).
• For plot styling: matplotlib, seaborn, plotly, plotnine, and SciencePlots via uv run --with (on-the-fly).
• For PDF conversion: poppler (brew install poppler on macOS)
• For presentations: agentic-presentation-builder (local clone)
• For BIDS validation: bids-validator (bunx bids-validator)
• For OCR: Mistral API key (optional, tesseract as offline fallback)

Skills vs commands

Skills are the preferred surface for agent-callable capabilities and auto-trigger from their description in Claude Code, Codex, and Copilot CLI. Commands are kept only for workflows that benefit from explicit /command args orchestration (epic/sprint management, project init, version bumps). Each plugin's skills are listed in the table above; describe your task in natural language and the matching skill will load.

Cross-agent instructions

Use AGENTS.md as the shared instruction file. CLAUDE.md imports it with @AGENTS.md, then leaves room for Claude Code-only plugin, skill, command, or MCP notes. The project plugin's init-project workflow now generates that layout for new projects.

Versioning

• Each plugin has independent versioning in its plugin.json
• Adding a new plugin/skill = marketplace minor bump (0.x.0)
• Version bump within an existing plugin = marketplace patch bump (0.x.y)

Notes

The opencite plugin included here is a snapshot of the standalone neuromechanist/opencite plugin. If you have already installed that standalone plugin, do not install it again from this marketplace; having both installed will create duplicate skills.

License

BSD-3-Clause