AlterLab Academic Skills

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Read in: [English](README.md) · [Türkçe](README.tr-TR.md)

🧬 210 purpose-built Claude AI skills for faculty, researchers & academicians Organized across 16 research domains — from Turkish academia to bioinformatics to digital humanities 210/210 ship executable evals · deterministic citation-existence verifier · per-domain bundles for claude.ai

Research Pipeline · Scientific Databases · Bioinformatics · Data Science · Visualization · Clinical Research · and more

Explore Skills » · Quick Start · Domain Overview · Contributing · Report Bug

Built by AlterLab Creative Technologies Laboratory

Not tied to any specific university — these skills work for any researcher, anywhere.

🎯 Plug & Play Drop a .md skill file intoClaude Projects or Claude Codeand get instant expertise

🧠 Domain Expert Each skill transforms Claudeinto a specialized researchassistant with deep knowledge

🔬 Real Frameworks Built on actual scientificmethods, tools, and professionaloutput templates

🌐 Universal Works for any researcherat any institution —no vendor lock-in

🚀 What's New in v2.2.0

• 🧠 Research-backed elevation of 191 skills — a corpus-wide accuracy and depth pass over every pre-existing skill: corrected regulation/API details, slimmed oversized bodies into references/, and version-bumped touched skills.
• 🧩 New core skill: Workflow Orchestration (alterlab-workflow-orchestration) — composes AlterLab skills into multi-agent workflows (subagent fan-out, pipelines, judge panels, adversarial verification), lifting the corpus to 210 skills. → [Core Pipeline](#-core-pipeline--9-skills)

• 🇹🇷 Turkish-academia flagship (12 skills) — the deepest Turkish-academia suite in any skills library: DergiPark, TR Dizin, YÖK Tez, YÖK Akademik, YÖKATLAS, TÜBİTAK 1001/1002-A proposals, doçentlik eligibility, akademik teşvik scoring, Turkish APA-7 style, TR research ethics, KVKK data-management plans, and TÜBİTAK Aperta — each wired to a verified national-platform endpoint. → [Turkish Academia](#-turkish-academia--national-platforms--scholarly-workflow-12-skills)
• 🎓 Faculty Life (6 skills) — syllabus AI policy, post-award grant reporting, recommendation letters, AACSB/ABET accreditation (AoL), REDCap/CDISC capture, and preprint deposition. → [Faculty Life](#-faculty-life--teaching-service--the-academic-career-6-skills)
• 🧪 Methodology (3 skills) — superpowers-style rigor (Iron Laws, Excuse-vs-Reality tables) applied to research methods: pre-registration discipline, statistical-test-selection guard, and results-reporting transparency. → [Methodology](#-methodology--research-rigor--discipline-gates-3-skills)
• 🧬 Bioinformatics grew 25 → 30 — production pipelines: nf-core/sarek variant calling, QIIME 2 amplicon, salmon/kallisto RNA-seq quant, NCBI BLAST+, and Squidpy spatial transcriptomics. → [Bioinformatics](#-bioinformatics--genomics-proteomics--molecular-biology-30-skills)
• ✅ Day-one evals on all 26 new skills — coverage stays 210 / 210; the shape + coverage gate runs in CI on every PR. → [docs/evals.md](docs/evals.md)

Previously — What's New in v2.0

• ✅ Full-corpus executable evals — schema + trigger-coverage are CI-gated on every PR; the behavioral pass (claude CLI + LLM judge) runs on demand via workflow_dispatch. → [docs/evals.md](docs/evals.md)
• 🔎 Deterministic citation-existence verifier that catches hallucinated references against Crossref / OpenAlex / Semantic Scholar / arXiv — no LLM guesswork in the gate. → [Headline feature](#-headline-feature--alterlab-citation-verifier)
• 📦 Per-domain claude.ai bundles on every Release — each dist/.zip clears the 200-file / 30 MB caps. → Releases
• 🌐 Live searchable catalog to browse every skill in the browser. → [Browse the Catalog](#-browse-the-catalog)
• 🤖 35 registered subagents + slash commands + a bundled academic MCP wiring PubMed / OpenAlex / Crossref / Zotero. → [MCP & Slash Commands](#-mcp--slash-commands)
• 📜 Honest provenance — upstream K-Dense fork credited in [THIRD_PARTY_NOTICES.md](THIRDPARTYNOTICES.md) and a machine-readable [CITATION.cff](CITATION.cff). → [Cite This Repository](#-cite-this-repository)

📋 Table of Contents

Click to expand / collapse

• [🚀 What's New in v2.2.0](#-whats-new-in-v220)
• [🎯 What Is This?](#-what-is-this)
• [🆕 v2.0 Highlights](#-v20-highlights)
• [✨ Key Features](#-key-features)
• [🗂️ Domain Overview](#%EF%B8%8F-domain-overview)
• [🔎 Browse the Catalog](#-browse-the-catalog)
• [🚀 Quick Start](#-quick-start)
• [⚡ Core Pipeline — 9 Skills](#-core-pipeline--9-skills)
• [📚 All 210 Skills](#-all-210-skills)
• [🏗️ Project Structure](#%EF%B8%8F-project-structure)
• [⚙️ How Skills Work](#%EF%B8%8F-how-skills-work)
• [💡 Usage Examples](#-usage-examples)
• [⚖️ How It Compares](#%EF%B8%8F-how-it-compares)
• [🤝 Contributing](#-contributing)
• [📖 Cite This Repository](#-cite-this-repository)
• [📜 License](#-license)
• [🙏 Credits](#-credits)

🎯 What Is This?

A comprehensive suite of 210 purpose-built Claude AI skills for faculty members, academicians, and researchers — organized into 16 domain categories spanning the full academic research lifecycle.

Each skill transforms Claude into a domain-specific expert assistant tailored to academic research, scientific computing, and scholarly publishing workflows.

> [!TIP] > How it works: Each skill is a structured SKILL.md file. Install the collection as a Claude Code plugin, or copy a skill directory into ~/.claude/skills/ (or a project's .claude/skills/) — and Claude becomes your research expert, with real scientific frameworks, professional output templates, and deep domain knowledge. A loose .md file does not auto-load.

🆕 v2.0 Highlights

> v2.0 is the "Trust & Reach" release — it turns the loudest objection to academic skills ("just prompts, no evals") into the headline differentiator.

| | What | Detail | |:---:|:---|:---| | ✅ | Executable evals across the corpus | 210 / 210 skills ship evals/evals.json on the canonical agentskills.io schema, validated in CI. See [docs/evals.md](docs/evals.md). | | 🔎 | Citation-existence verifier | New core skill alterlab-citation-verifier — a deterministic gate that checks every reference actually exists against four keyless scholarly APIs (Crossref, OpenAlex, Semantic Scholar, arXiv), flags retractions, and maps claim-faithfulness verdicts. See below. | | 📦 | Per-domain bundles for claude.ai | dist/.zip bundles (one per domain) attached to each Release — each clears claude.ai's 200-file / 30 MB caps and vendors the shared handoff contracts. | | 🔌 | Bundled academic MCP | The core and databases plugins ship a .mcp.json wiring PubMed / OpenAlex / Crossref / Zotero, with a documented requests/ fallback when no MCP is available. | | ⌨️ | Slash commands | /lit-review, /review-paper, /cite-check, /research-pipeline — drive the core pipeline directly. | | 🗂️ | Generated catalog | A machine-readable [skills.json](skills.json) is generated from skill frontmatter; a CI gate keeps every count in this README honest. | | 📜 | Honest provenance | Upstream K-Dense fork credited in [THIRD_PARTY_NOTICES.md](THIRDPARTYNOTICES.md) + [PROVENANCE.md](PROVENANCE.md) / [CITATION.cff](CITATION.cff). |

🔎 Headline feature — alterlab-citation-verifier

Around 147 k hallucinated citations surfaced in published work in 2025. Prompt-only "fact-checking" misses roughly a third of them. alterlab-citation-verifier is a deterministic core capability that, for every entry in a bibliography:

• cross-checks existence against Crossref + OpenAlex + Semantic Scholar + arXiv (all keyless),
• resolves DOIs / arXiv IDs and matches title + author with a Levenshtein threshold,
• flags Retraction Watch entries,
• maps each verdict to the suite's TF / PAC / IH / PH / SH faithfulness taxonomy,

and degrades gracefully to plain requests / WebSearch when no MCP or network is present. It rewires the pipeline's bibliography and integrity agents to call it instead of generic web search.

✨ Key Features

| | Feature | Description | |:---:|:---|:---| | 🔬 | Research-Ready | Skills built on real scientific methods, databases, and professional frameworks used by working researchers | | 🤖 | Multi-Agent Pipelines | Core skills chain together: Research → Write → Review → Publish in a seamless workflow | | 📊 | 39 Database Integration Skills | Instant access to PubMed, ChEMBL, UniProt, ClinicalTrials.gov, COSMIC, and more | | 🧬 | Deep Domain Coverage | From single-cell RNA-seq analysis to quantum computing, from clinical trials to digital humanities | | 📝 | Publication-Quality Output | LaTeX papers, conference posters, grant proposals, scientific visualizations — all formatted to professional standards | | 🔄 | Mix & Match | Combine multiple skills in one Claude Project for a multi-expert research team |

🗂️ Domain Overview

| | Domain | Skills | Focus Areas | |:---:|:---|:---:|:---| | 🔄 | Core Pipeline | 9 | Multi-agent research → write → review → publish pipeline + citation verifier + teaching + thesis + workflow orchestration | | 🗄️ | Databases | 39 | Connectors to scientific databases — PubMed, ChEMBL, UniProt, ClinicalTrials.gov, COSMIC, and more | | 🧬 | Bioinformatics | 30 | Genomics, proteomics, molecular biology — Scanpy, BioPython, ESM, single-cell analysis, nf-core/sarek, QIIME 2, RNA-seq quant | | ⚗️ | Cheminformatics | 12 | Chemistry and drug discovery — RDKit, molecular dynamics, docking, ADMET | | 🏥 | Clinical Research | 7 | Clinical decision support, treatment planning, medical imaging, regulatory | | 📊 | Data Science | 22 | ML/statistics — scikit-learn, PyTorch Lightning, SHAP, transformers | | 📈 | Visualization | 8 | Scientific plotting — Matplotlib, Seaborn, Plotly, schematics, infographics | | ✍️ | Writing Tools | 13 | Scientific writing, citations, grants, posters, academic career | | 🔧 | Lab Integrations | 9 | Laboratory platforms — Benchling, DNAnexus, Opentrons, Protocols.io | | 🌍 | Domain-Specific | 17 | Quantum computing, geospatial, materials science, social science methods, digital humanities | | 📄 | Document Tools | 2 | Markdown & document conversion — MarkItDown, Open Notebook | | 🔍 | Research Tools | 14 | Search, discovery, Zotero, citation graphs, PDF evidence tables, qualitative methods, ethics, surveys, open science | | 💰 | Finance & Economics | 7 | FRED, Alpha Vantage, SEC EDGAR, market research | | 🇹🇷 | Turkish Academia | 12 | National platforms & scholarly workflow — DergiPark, TR Dizin, YÖK Tez/Akademik, YÖKATLAS, TÜBİTAK proposals, doçentlik, teşvik, KVKK, Aperta | | 🎓 | Faculty Life | 6 | Teaching, service & the academic career — syllabus AI policy, grant reporting, recommendation letters, accreditation, REDCap/CDISC, preprints | | 🧪 | Methodology | 3 | Research-rigor discipline gates — pre-registration, test-selection guard, results-reporting transparency |

🔎 Browse the Catalog

Search all 210 skills by name, domain, or keyword — no install required.

🚀 Quick Start

🌍 Option 1 — Agent Skills (open standard) (Recommended)

npx skills add AlterLab-IEU/AlterLab-Academic-Skills

These are portable Agent Skills following the agentskills.io open standard — they also work in Cursor, Codex, Gemini CLI, and Copilot, not Claude only.

> [!NOTE] > Standard: Agent Skills. This collection conforms to the open Agent Skills standard. See agentskills.io for the spec and the list of supporting agents.

⚡ Option 2 — Claude Code Plugin

Add the marketplace once, then install only the domains you need:

/plugin marketplace add AlterLab-IEU/AlterLab-Academic-Skills
# No SSH key? Use the HTTPS marketplace path instead:
/plugin marketplace add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git
/plugin install alterlab-bioinformatics@alterlab-academic-skills
/reload-plugins

For local development against a clone, point Claude Code at the directory directly:

claude --plugin-dir /path/to/AlterLab-Academic-Skills

Available domain plugins: alterlab-core, alterlab-databases, alterlab-bioinformatics, alterlab-cheminformatics, alterlab-clinical-research, alterlab-data-science, alterlab-visualization, alterlab-writing-tools, alterlab-lab-integrations, alterlab-domain-specific, alterlab-document-tools, alterlab-research-tools, alterlab-finance-economics, alterlab-turkish-academia, alterlab-faculty-life, alterlab-methodology.

📁 Option 3 — Personal or Project Install (manual)

git clone https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git
# Personal — available in every project:
cp -R AlterLab-Academic-Skills/skills/bioinformatics/alterlab-scanpy ~/.claude/skills/
# Project-scoped — only in the current repo:
cp -R AlterLab-Academic-Skills/skills/bioinformatics/alterlab-scanpy .claude/skills/

Then restart Claude Code. A skill must live at ~/.claude/skills//SKILL.md or .claude/skills//SKILL.md — a bare git clone alone does not register anything.

🌐 Option 4 — Claude.ai (per-domain bundles)

Every Release ships pre-built dist/.zip bundles. Each is spec-conformant and clears claude.ai's 200-file / 30 MB caps, and vendors the shared handoff contracts so cross-skill references resolve.

1. Download the domain bundle you need from the Releases page — e.g. bioinformatics.zip, databases.zip, core.zip.
2. Upload it under Settings → Capabilities (requires a plan with code execution).

Skills do not sync between claude.ai and Claude Code. To zip a single skill yourself instead, archive its directory (zip -r alterlab-scanpy.zip skills/bioinformatics/alterlab-scanpy).

🛠️ Option 5 — install.sh (scriptable local install)

The bundled installer copies whole domains and/or individual skills into the right local directory (~/.claude/skills/ or the cross-tool ~/.agents/skills/), idempotently:

git clone https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git
cd AlterLab-Academic-Skills

scripts/install.sh --list                         # show every domain / skill
scripts/install.sh bioinformatics                 # whole domain
scripts/install.sh databases/alterlab-pubmed      # one skill
scripts/install.sh --project core                 # into ./.claude/skills
scripts/install.sh                                 # install everything

Then restart your agent to load them.

🔌 MCP & Slash Commands

The core and databases plugins ship a .mcp.json that wires the PubMed / OpenAlex / Crossref / Zotero academic MCP servers, with a documented requests/ fallback when no MCP host is available — so the citation verifier and database skills work online or offline. Install either plugin (Option 2) to pick the MCP up automatically.

Installing the core plugin also registers these slash commands:

| Command | Drives | |:---|:---| | /lit-review | alterlab-deep-research — systematic literature review | | /review-paper | alterlab-paper-reviewer — multi-perspective peer review | | /cite-check | alterlab-citation-verifier — deterministic citation-existence gate | | /research-pipeline | alterlab-research-pipeline — full research → publish orchestrator |

> [!NOTE] > 210 / 210 skills ship executable evals on

…

Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: AlterLab-IEU
• Source: AlterLab-IEU/AlterLab-Academic-Skills
• License: MIT
• Homepage: https://alterlab-ieu.github.io/AlterLab-Academic-Skills/

Install and usage instructions live in the source repository linked above.