research-skills

In the author's own words, from each skill's SKILL.md — showing the first 30 of 37 files.

• ai-full-figure

  Use this skill when the user asks to "generate an AI figure", "make an AI-generated figure", "make a poster figure", "make a presentation figure", "generate a figure with AI", "generate figure panels with Codex", "make a multi-panel AI figure", "AI background for a figure", or wants a pictorial figure or panel (brain scene, apparatus, anatomy, pipeline illustration) rendered by gpt-image-2 throug…

  plugins/figures/skills/ai-full-figure/SKILL.md on GitHub (opens in a new tab)

• figure-bible

  Use this skill when the user asks to "make a figure bible", "set up a style bible", "create a figure theme", "make a theme for my figures", "set up a figure style", "palette for my paper figures", or wants a consistent figure style. Scaffolds and validates figures/theme.json; run before any figures skill generates images.

  plugins/figures/skills/figure-bible/SKILL.md on GitHub (opens in a new tab)

• figure-qa

  Use this skill to QA a scientific figure for journal compliance, alignment, palette correctness, and text legibility. Triggers on "QA this figure", "check this figure", "review my figure", "is this figure paper-ready", "validate figure", "check the text in this figure", or when invoked after a figures skill produces output (unless the caller passes no-qa). Dispatches on input type (SVG, raster PN…

  plugins/figures/skills/figure-qa/SKILL.md on GitHub (opens in a new tab)

• plot-styling

  This skill should be used when the user asks to "plot data", "make a plot for a paper", "make a publication plot", "create a journal-quality plot", "matplotlib for a figure", "use seaborn", "use plotnine", "use ggplot in Python", "improve plot quality", "style my plot", "clean up my figure", "my matplotlib plot looks ugly", "apply journal style to existing script", "fix matplotlib defaults", "use…

  plugins/figures/skills/plot-styling/SKILL.md on GitHub (opens in a new tab)

• scientific-figure

  This skill should be used when the user asks to "create a figure", "make a scientific figure", "create a paper figure", "make a figure for my paper", "make a figure for my manuscript", "compose figure panels", "assemble figure panels", "combine figure panels", "make a multi-panel figure", "figure composition", "export a figure", "generate a PDF figure", "create a Nature-style figure", "make a jou…

  plugins/figures/skills/scientific-figure/SKILL.md on GitHub (opens in a new tab)

• svg-figure

  This skill should be used when the user asks to "create an SVG figure", "make a schematic", "draw a diagram", "create a schematic diagram", "draw a flowchart", "draw a process flow", "draw a workflow", "draw a workflow diagram", "make an SVG schematic", "create a process diagram", "create a pipeline diagram", "create a block diagram", "draw a system diagram", "system architecture diagram", "make…

  plugins/figures/skills/svg-figure/SKILL.md on GitHub (opens in a new tab)

• svg-primitives

  Use when the user asks to build a programmatic SVG schematic in Python: flowcharts, boxes and arrows, auto-fit SVG text, mm-precise diagrams, edge-snapped arrows, tangent-correct curve arrowheads, orthogonal or Manhattan routing, deterministic z-order layers, labeled groups, bracket groupings, leader-line annotations, or strict Canvas.save validation for text overflow. Use figure-qa instead for a…

  plugins/figures/skills/svg-primitives/SKILL.md on GitHub (opens in a new tab)

• transparent-icons

  Use this skill when the user asks to "make an icon", "generate an icon", "create a scientific icon", "make a transparent icon", "make a minimal icon", "icon for a figure", "icon for a paper", "generate an icon set", "batch icons", or wants flat scientific icons (brain, neuron, DNA, EEG cap, microscope) with transparent backgrounds in a journal style. Generates PNG icons with gpt-image-2 through t…

  plugins/figures/skills/transparent-icons/SKILL.md on GitHub (opens in a new tab)

• grant-figure-qa

  Use this skill to review grant proposal figures for compliance, resolution, accessibility, and quality. Triggers on "check grant figures", "review proposal figures", "figure QA for grant", "NIH figure requirements", or when preparing a grant for submission.

  plugins/grant/skills/grant-figure-qa/SKILL.md on GitHub (opens in a new tab)

• grant-review

  This skill should be used when the user asks to "review a grant", "review my proposal", "score this grant", "evaluate my specific aims", "critique my research strategy", "review as an NIH reviewer", "review as an NSF panelist", "give me reviewer feedback", "check my grant proposal", "review my R01", "review my K99", "review my SBIR", "review my STTR", "review my Phase I application", "review my P…

  plugins/grant/skills/grant-review/SKILL.md on GitHub (opens in a new tab)

• grant-writing

  This skill should be used when the user asks to "write a grant proposal", "draft specific aims", "write a research strategy", "create an NIH proposal", "create an NSF proposal", "write a significance section", "write an innovation section", "write an approach section", "draft a DP2 essay", "write an R01", "write an R21", "write a K99", "write an R03", "write a K08", "write a K23", "write an F31",…

  plugins/grant/skills/grant-writing/SKILL.md on GitHub (opens in a new tab)

• humanizer

  Use this skill for "humanize this text", "remove AI tells", "make this less AI-sounding", "strip AI patterns", "de-AI my writing", "reduce AI-isms", "final natural-writing pass", "check for AI vocabulary", "em dash overuse", "rule of three overuse", "AI vocabulary", "signs of AI writing", or when polishing prose (papers, grants, lit reviews, abstracts, cover letters, responses to reviewers) to re…

  plugins/manuscript/skills/humanizer/SKILL.md on GitHub (opens in a new tab)

• lit-review

  Use this skill for "literature review workflow", "multi-phase lit review", "direction paper", "review paper protocol", "strand-based literature review", "citation-grounded review", "systematic lit review with paper cards", "build a lit review corpus", "lit review pipeline", "orchestrate a literature review", "research directions document", "write a literature review", "synthesize papers", "themat…

  plugins/manuscript/skills/lit-review/SKILL.md on GitHub (opens in a new tab)

• manuscript-formatting

  Use this skill for "format manuscript", "prepare for submission", "journal formatting", "LaTeX template", "submission checklist", "format references", "BibTeX", "author guidelines", "page limits", "format for Nature", "format for IEEE", or when the user wants to format a manuscript for journal submission.

  plugins/manuscript/skills/manuscript-formatting/SKILL.md on GitHub (opens in a new tab)

• manuscript-writing

  Use this skill for "write a paper", "draft manuscript", "write introduction", "write methods section", "write results", "write discussion", "write abstract", "structure a paper", "academic writing", "write for journal", or when the user wants to draft or revise sections of an academic manuscript.

  plugins/manuscript/skills/manuscript-writing/SKILL.md on GitHub (opens in a new tab)

• paper-review

  Use this skill for "review this paper", "review this manuscript", "peer review", "review my paper", "critique this manuscript", "review this submission", "give me feedback on my paper", "check my methods", "review my statistics", "review as a peer reviewer", "evaluate this manuscript", "review this PDF", or mentions manuscript review, peer review, paper critique, or methodological review.

  plugins/manuscript/skills/paper-review/SKILL.md on GitHub (opens in a new tab)

• runpod

  This skill should be used when the user says "spin up a RunPod pod", "rent a GPU", "run this on a cloud GPU", "RunPod", "prebake a GPU image", "my pod takes 10 minutes to install", "boot-to-ready", "which GPU should I rent", "2x A100 or 1x H100", "is Modal cheaper", "multi-GPU pod", "fan out this grid across pods", "run the benchmark in parallel", "pod fleet", "only one pod launched", "pod ssh pe…

  plugins/ml-training/skills/runpod/SKILL.md on GitHub (opens in a new tab)

• bids-conversion

  Use this skill for "convert to BIDS", "BIDS format", "create BIDS dataset", "BIDS sidecar", "participants.tsv", "events.tsv", "EEG BIDS", "EMG BIDS", "MEG BIDS", "fMRI BIDS", "BIDS validator", "channel locations", "electrode positions", "BIDS metadata", or when the user wants to convert neuroscience data to Brain Imaging Data Structure (BIDS) format or validate BIDS compliance.

  plugins/neuroinformatics/skills/bids-conversion/SKILL.md on GitHub (opens in a new tab)

• experiment-design

  Use this skill for "design experiment", "create PsychoPy experiment", "stimulus presentation", "experiment protocol", "timing validation", "trial structure", "block design", "event-related design", "PsychoPy builder", "create stimuli", "LSL markers", "Lab Streaming Layer", "event markers", "trigger codes", or when the user wants to design or implement a neuroscience experiment.

  plugins/neuroinformatics/skills/experiment-design/SKILL.md on GitHub (opens in a new tab)

• opencite

  Use this skill for "search for papers", "find citations", "look up a DOI", "get BibTeX", "download PDF", "convert PDF to markdown", "find canonical papers", "convert identifiers", "batch download papers", "configure opencite", "literature review", "find related papers", "what papers cite this", "export references", "read this paper", or mentions of opencite, Semantic Scholar, OpenAlex, PubMed, ac…

  plugins/opencite/skills/opencite/SKILL.md on GitHub (opens in a new tab)

• presentation-builder

  This skill should be used when the user asks to "create a presentation", "make slides", "build a slide deck", "create a talk", "make a keynote", "create a Reveal.js presentation", "generate presentation slides", "make a conference talk", "create a lecture", "build a poster presentation", "create presentation JSON", or mentions presentations, slides, slide decks, Reveal.js, talk preparation, confe…

  plugins/presentation/skills/presentation-builder/SKILL.md on GitHub (opens in a new tab)

• agent-fanout

  Use this skill when the user asks to "fan out agents", "spawn agents", "use an agent team", "parallel agents", "delegate to subagents", "act as team lead", "orchestrate implementation", "fan out teammates", or when a task decomposes into 2+ independent work items (parallel exploration, one implementer per issue, a multi-lens PR review panel). Covers the basic mechanics of spawning, briefing, supe…

  plugins/project/skills/agent-fanout/SKILL.md on GitHub (opens in a new tab)

• ci-scaffolding

  This skill should be used when the user says "set up CI", "create GitHub Actions", "scaffold CI pipeline", "add CI/CD", "configure continuous integration", "create test workflow", "create release workflow", "add pre-commit hooks", "set up linting pipeline", "configure ruff in CI", "configure biome in CI", "add typo checking", or wants to add, update, or customize CI/CD pipelines for their project…

  plugins/project/skills/ci-scaffolding/SKILL.md on GitHub (opens in a new tab)

• codebase-onboarding

  Use this skill when the user asks to "explore this codebase", "understand this repo", "map the architecture", "review our stack", "get up to speed", "break ground" on an unfamiliar project or research field, "what is the state of this project", "audit the architecture", or before planning changes in a codebase you have not worked in. Produces a verified reconnaissance report before any design or…

  plugins/project/skills/codebase-onboarding/SKILL.md on GitHub (opens in a new tab)

• debugging

  Use this skill when the user asks to "debug", "find the root cause", "figure out why X fails", "investigate this bug", "this test is flaky", "the build broke", "production incident", "why is the output wrong", or when any observed behavior contradicts expected behavior. Covers the reproduce-isolate-prove-fix-verify loop, anti-shortcut gates, and numerical/scientific debugging.

  plugins/project/skills/debugging/SKILL.md on GitHub (opens in a new tab)

• docker-packaging

  This skill should be used when the user says "create Dockerfile", "dockerize project", "Docker packaging", "container setup", "multi-stage build", "Docker Compose", "containerize application", "create docker-compose.yml", "create .dockerignore", "optimize Docker image", or wants to containerize their project or create Docker configurations.

  plugins/project/skills/docker-packaging/SKILL.md on GitHub (opens in a new tab)

• document-processing

  This skill should be used when the user says "process documents", "extract text from PDF", "OCR this document", "convert PDF to markdown", "extract emails from documents", "parse document", "document conversion", "batch OCR", "extract structured data from PDF", "read PDF", "extract tables from PDF", "convert Word document", "convert docx to markdown", or wants to extract, convert, or process docu…

  plugins/project/skills/document-processing/SKILL.md on GitHub (opens in a new tab)

• engineering-loop

  Use this skill when the user asks to "implement this change", "fix this issue", "add this feature", "make this change properly", "ship this", or for any ordinary single-PR development task: one issue, one branch, one pull request. For multi-phase features use epic-dev; for unfamiliar code run codebase-onboarding first; for failing behavior use the debugging skill.

  plugins/project/skills/engineering-loop/SKILL.md on GitHub (opens in a new tab)

• epic-dev

  Execute the project epic development workflow for Codex. Use when the user asks for "epic dev", "epic-dev", "/epic-dev", "run the epic workflow", "create an epic", "resume the epic", "--resume", "--next-phase", "--finalize", phased feature delivery, sprint phases, GitHub sub-issues, or git worktrees for multi-phase implementation.

  plugins/project/skills/epic-dev/SKILL.md on GitHub (opens in a new tab)

• implementation-planning

  Use this skill when the user asks to "plan this feature", "write an implementation plan", "design before coding", "think through the approach", "review this plan", or before any multi-file change, architectural decision, experiment with a go/no-go outcome, or strategic pivot. Produces a verifiable plan with pre-registered decision gates and an explicit list of open judgment calls.

  plugins/project/skills/implementation-planning/SKILL.md on GitHub (opens in a new tab)

No skill matches that filter.

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