Install
$ npx skills add AlterLab-IEU/AlterLab-Academic-SkillsREADME
# GitHub Repository: AlterLab-IEU/AlterLab-Academic-Skills
**URL:** https://github.com/AlterLab-IEU/AlterLab-Academic-Skills
**Author:** AlterLab-IEU
**Description:** 210 evaluated academic Claude/agent skills across 16 research domains — bioinformatics, cheminformatics, data science, databases, clinical, Turkish academia & more. Every skill ships an executable eval (agentskills.io schema). Citation verifier + research→write→review→publish pipeline. Claude Code, Cursor, Codex, Gemini CLI & Copilot.
**Homepage:** https://alterlab-ieu.github.io/AlterLab-Academic-Skills/
**Language:** Python
## Stats
- Stars: 28
- Forks: 5
- Open Issues: 2
- Commits: 67
- Created: 2026-03-16T15:24:02Z
- Updated: 2026-06-18T11:36:53Z
- Pushed: 2026-06-12T13:48:47Z
## README
<div align="center">
<img src=".github/header-banner.svg" width="100%" alt="AlterLab Academic Skills">
<br>
<a href="skills/"><img src="https://img.shields.io/badge/Skills-210-7C3AED?style=for-the-badge&logo=bookstack&logoColor=white" alt="Skills"></a>
<a href="skills/"><img src="https://img.shields.io/badge/Domains-16-2563EB?style=for-the-badge&logo=databricks&logoColor=white" alt="Domains"></a>
<a href="docs/evals.md"><img src="https://img.shields.io/badge/Evals-210%2F210-16A34A?style=for-the-badge&logo=checkmarx&logoColor=white" alt="Eval coverage"></a>
<a href="https://www.anthropic.com"><img src="https://img.shields.io/badge/Claude-AI%20Powered-F97316?style=for-the-badge&logo=anthropic&logoColor=white" alt="Claude AI"></a>
<a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-10B981?style=for-the-badge&logo=opensourceinitiative&logoColor=white" alt="MIT License"></a>
<a href="https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/releases"><img src="https://img.shields.io/github/v/release/AlterLab-IEU/AlterLab-Academic-Skills?style=for-the-badge&logo=github&color=8B5CF6&logoColor=white&label=Release" alt="Release"></a>
<a href="https://agentskills.io"><img src="https://img.shields.io/badge/Agent%20Skills-Open%20Standard-0EA5E9?style=for-the-badge&logo=anthropic&logoColor=white" alt="Agent Skills — open standard"></a>
<br>
<a href="https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/stargazers"><img src="https://img.shields.io/github/stars/AlterLab-IEU/AlterLab-Academic-Skills?style=for-the-badge&logo=github&color=EAB308&logoColor=white" alt="Stars"></a>
<a href="https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/network/members"><img src="https://img.shields.io/github/forks/AlterLab-IEU/AlterLab-Academic-Skills?style=for-the-badge&logo=git&color=6366F1&logoColor=white" alt="Forks"></a>
<a href="https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/issues"><img src="https://img.shields.io/github/issues/AlterLab-IEU/AlterLab-Academic-Skills?style=for-the-badge&logo=github&color=EF4444&logoColor=white" alt="Issues"></a>
<a href="CONTRIBUTING.md"><img src="https://img.shields.io/badge/PRs-Welcome-22C55E?style=for-the-badge&logo=githubactions&logoColor=white" alt="PRs Welcome"></a>
<a href="https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/actions/workflows/pytest.yml"><img src="https://img.shields.io/github/actions/workflow/status/AlterLab-IEU/AlterLab-Academic-Skills/pytest.yml?branch=main&style=for-the-badge&logo=githubactions&logoColor=white&label=tests" alt="Tests"></a>
<a href="https://github.com/BehiSecc/awesome-claude-skills"><img src="https://awesome.re/badge.svg" alt="Awesome"></a>
<br>
> 📢 **Featured in** [awesome-claude-skills](https://github.com/BehiSecc/awesome-claude-skills) (5.7k ⭐)
<br>
**Read in:** [English](README.md) · [Türkçe](README.tr-TR.md)
<br><br>
<h3>🧬 210 purpose-built Claude AI skills for faculty, researchers & academicians</h3>
<p><em>Organized across 16 research domains — from Turkish academia to bioinformatics to digital humanities</em></p>
<p><em>210/210 ship executable evals · deterministic citation-existence verifier · per-domain bundles for claude.ai</em></p>
<p>
<b>Research Pipeline</b> · <b>Scientific Databases</b> · <b>Bioinformatics</b> · <b>Data Science</b> · <b>Visualization</b> · <b>Clinical Research</b> · <b>and more</b>
</p>
<p>
<a href="skills/"><b>Explore Skills »</b></a> ·
<a href="#-quick-start">Quick Start</a> ·
<a href="#%EF%B8%8F-domain-overview">Domain Overview</a> ·
<a href="CONTRIBUTING.md">Contributing</a> ·
<a href="https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/issues">Report Bug</a>
</p>
<br>
<hr>
<table><tr><td>
<b>Built by</b> <a href="https://github.com/AlterLab-IEU"><b>AlterLab Creative Technologies Laboratory</b></a>
<br><br>
<em>Not tied to any specific university — these skills work for any researcher, anywhere.</em>
</td></tr></table>
</div>
<br>
<!-- FEATURE HIGHLIGHTS -->
<div align="center">
<table>
<tr>
<td align="center" width="25%">
<h3>🎯</h3>
<h3>Plug & Play</h3>
<p>Drop a <code>.md</code> skill file into<br>Claude Projects or Claude Code<br>and get instant expertise</p>
</td>
<td align="center" width="25%">
<h3>🧠</h3>
<h3>Domain Expert</h3>
<p>Each skill transforms Claude<br>into a specialized research<br>assistant with deep knowledge</p>
</td>
<td align="center" width="25%">
<h3>🔬</h3>
<h3>Real Frameworks</h3>
<p>Built on actual scientific<br>methods, tools, and professional<br>output templates</p>
</td>
<td align="center" width="25%">
<h3>🌐</h3>
<h3>Universal</h3>
<p>Works for any researcher<br>at any institution —<br>no vendor lock-in</p>
</td>
</tr>
</table>
</div>
<br>
## 🚀 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)
<details>
<summary><b>Previously — What's New in v2.0</b></summary>
<br>
- ✅ **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/<domain>.zip` clears the 200-file / 30 MB caps. → [Releases](https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/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`](THIRD_PARTY_NOTICES.md) and a machine-readable [`CITATION.cff`](CITATION.cff). → [Cite This Repository](#-cite-this-repository)
</details>
<br>
## 📋 Table of Contents
<details open>
<summary><b>Click to expand / collapse</b></summary>
<br>
- [🚀 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)
</details>
<br>
## 🎯 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.
<br>
## 🆕 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](https://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/<domain>.zip` bundles (one per domain) attached to each [Release](https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/releases) — 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`](THIRD_PARTY_NOTICES.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.
<br>
## ✨ 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 |
<br>
## 🗂️ 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 |
<br>
## 🔎 Browse the Catalog
<div align="center">
<a href="https://alterlab-ieu.github.io/AlterLab-Academic-Skills/"><img src="https://img.shields.io/badge/Browse%20the%20Catalog-Live%20%26%20Searchable-7C3AED?style=for-the-badge&logo=readthedocs&logoColor=white" alt="Browse the live searchable catalog"></a>
<em>Search all 210 skills by name, domain, or keyword — no install required.</em>
</div>
<br>
## 🚀 Quick Start
### 🌍 Option 1 — Agent Skills (open standard) *(Recommended)*
```bash
npx skills add AlterLab-IEU/AlterLab-Academic-Skills
```
These are portable **Agent Skills** following the [agentskills.io](https://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](https://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:
```bash
/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:
```bash
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)
```bash
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/<name>/SKILL.md` or `.claude/skills/<name>/SKILL.md` — a bare `git clone` alone does **not** register anything.
### 🌐 Option 4 — Claude.ai (per-domain bundles)
Every Release ships pre-built **`dist/<domain>.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](https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/releases) — 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:
```bash
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 |
<br>
> [!NOTE]
> **210 / 210 skills ship executable evals** on the canonical [agentskills.io](https://agentskills.io) schema. Schema and trigger-coverage are validated in CI on every PR; the behavioral pass (claude CLI + LLM judge) runs on demand via `workflow_dispatch`. See [`docs/evals.md`](docs/evals.md) for how coverage is measured and how to run `scripts/run_evals.py` locally.
<br>
---
## ⚡ Core Pipeline — 9 Skills
> *The heart of the system — a multi-agent research-to-publication pipeline with 39 specialized agents, plus teaching and thesis supervision tools.*
| # | Skill | Agents | What It Does |
|:---:|:---|:---:|:---|
| 1 | **🔬 Deep Research** | 13 | Multi-mode research with systematic review, Socratic dialogue, fact-checking |
| 2 | **📝 Paper Writer** | 12 | Academic paper authoring with LaTeX, bilingual support, 9 writing modes |
| 3 | **🔍 Paper Reviewer** | 7 | Multi-perspective peer review with Devil's Advocate, 0–100 quality rubrics |
| 4 | **🔄 Research Pipeline** | 7 | 10-stage orchestrator with integrity verification and material passports |
| 5 | **🔎 Citation Verifier** | — | Deterministic citation-existence gate over Crossref / OpenAlex / Semantic Scholar / arXiv |
| 6 | **🎓 Teaching Design** | — | Course design, syllabi, rubrics, Bloom's taxonomy, backward design |
| 7 | **📋 Thesis Supervisor** | — | Dissertation guidance, defense prep, committee management |
| 8 | **🔗 Link Health** | — | Repo link-health audit meta-skill |
| 9 | **🧩 Workflow Orchestration** | — | Composes AlterLab skills into multi-agent workflows: subagent fan-out, pipelines, judge panels, adversarial verification |
<br>
---
## 📚 All 210 Skills
### 🗄️ Databases — Scientific Database Connectors (39 Skills)
<details>
<summary><b>Click to expand full database skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **AlphaFold DB** | Protein structure predictions from AlphaFold |
| 2 | **arXiv** | Preprint search and discovery |
| 3 | **BindingDB** | Binding affinity data for drug-target interactions |
| 4 | **bioRxiv** | Biology preprint search and monitoring |
| 5 | **BRENDA** | Enzyme functional data |
| 6 | **cBioPortal** | Cancer genomics data exploration |
| 7 | **ChEMBL** | Bioactive molecules with drug-like properties |
| 8 | **ClinicalTrials.gov** | Clinical trial registry search |
| 9 | **ClinPGx** | Clinical pharmacogenomics data |
| 10 | **ClinVar** | Genomic variation and human health |
| 11 | **COSMIC** | Catalogue of somatic mutations in cancer |
| 12 | **Data Commons** | Google's open knowledge graph |
| 13 | **DepMap** | Cancer dependency mapping |
| 14 | **DrugBank** | Drug and drug target information |
| 15 | **ENA** | European Nucleotide Archive |
| 16 | **Ensembl** | Genome annotation and variation |
| 17 | **FDA** | FDA drug and device data |
| 18 | **Gene DB** | Gene-level data aggregation |
| 19 | **GEO** | Gene Expression Omnibus datasets |
| 20 | **gnomAD** | Genome aggregation and variant frequency |
| 21 | **GTEx** | Tissue-specific gene expression |
| 22 | **GWAS Catalog** | Genome-wide association studies |
| 23 | **HMDB** | Human Metabolome Database |
| 24 | **Imaging Data Commons** | Cancer imaging data |
| 25 | **InterPro** | Protein families and domains |
| 26 | **JASPAR** | Transcription factor binding profiles |
| 27 | **KEGG** | Biological pathways and networks |
| 28 | **Metabolomics Workbench** | Metabolomics data repository |
| 29 | **Monarch Initiative** | Disease-gene associations |
| 30 | **OpenAlex** | Open scholarly metadata |
| 31 | **Open Targets** | Drug target identification |
| 32 | **PDB** | Protein 3D structure database |
| 33 | **PubChem** | Chemical information database |
| 34 | **PubMed** | Biomedical literature search |
| 35 | **Reactome** | Biological pathway database |
| 36 | **STRING** | Protein-protein interaction networks |
| 37 | **UniProt** | Protein sequence and function |
| 38 | **USPTO** | Patent search and analysis |
| 39 | **ZINC** | Commercially-available compounds for docking |
</details>
### 🧬 Bioinformatics — Genomics, Proteomics & Molecular Biology (30 Skills)
<details>
<summary><b>Click to expand full bioinformatics skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **AnnData** | Annotated data matrices for single-cell |
| 2 | **Arboreto** | Gene regulatory network inference |
| 3 | **BioPython** | General-purpose bioinformatics toolkit |
| 4 | **BioServices** | Programmatic access to biological web services |
| 5 | **CellxGene** | Interactive single-cell data exploration |
| 6 | **COBRApy** | Constraint-based metabolic modeling |
| 7 | **deepTools** | NGS data analysis and visualization |
| 8 | **ESM** | Protein language models |
| 9 | **ETE Toolkit** | Phylogenetic tree analysis and visualization |
| 10 | **FlowIO** | Flow cytometry data handling |
| 11 | **gget** | Query genomic databases from Python |
| 12 | **Glycoengineering** | Glycan analysis and engineering |
| 13 | **HistoLab** | Computational histopathology |
| 14 | **LaminDB** | Data lineage and biological data management |
| 15 | **Neuropixels** | Neural probe data processing |
| 16 | **PathML** | Machine learning for pathology |
| 17 | **Phylogenetics** | Evolutionary tree construction |
| 18 | **PyDESeq2** | Differential gene expression analysis |
| 19 | **pyOpenMS** | Mass spectrometry data analysis |
| 20 | **pysam** | SAM/BAM file manipulation |
| 21 | **Scanpy** | Single-cell analysis in Python |
| 22 | **scikit-bio** | Bioinformatics algorithms and data structures |
| 23 | **scVelo** | RNA velocity analysis |
| 24 | **scvi-tools** | Deep generative models for single-cell |
| 25 | **TileDB-VCF** | Population-scale genomic variant storage |
| 26 | **BLAST** | NCBI BLAST+ command-line sequence similarity searches |
| 27 | **nf-core/sarek** | FASTQ-to-VCF germline & somatic variant-calling pipeline |
| 28 | **QIIME 2 Amplicon** | 16S/ITS microbiome amplicon analysis |
| 29 | **RNA-seq Quant** | Transcript abundance with salmon & kallisto |
| 30 | **Squidpy Spatial** | Spatial transcriptomics on AnnData/SpatialData |
</details>
### ⚗️ Cheminformatics — Chemistry & Drug Discovery (12 Skills)
<details>
<summary><b>Click to expand full cheminformatics skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **Datamol** | Molecular data manipulation |
| 2 | **DeepChem** | Deep learning for chemistry |
| 3 | **DiffDock** | Diffusion-based molecular docking |
| 4 | **matchms** | Mass spectra matching and similarity |
| 5 | **MedChem** | Medicinal chemistry analysis |
| 6 | **Molecular Dynamics** | MD simulation setup and analysis |
| 7 | **MolFeat** | Molecular featurization |
| 8 | **PrimeKG** | Precision medicine knowledge graph |
| 9 | **PyTDC** | Therapeutics Data Commons access |
| 10 | **RDKit** | Core cheminformatics toolkit |
| 11 | **Rowan** | Computational chemistry workflows |
| 12 | **TorchDrug** | Graph neural networks for drug discovery |
</details>
### 🏥 Clinical Research — Clinical Decision Support & Medical Tools (7 Skills)
<details>
<summary><b>Click to expand full clinical research skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **Clinical Decision** | Evidence-based clinical decision support |
| 2 | **Clinical Reports** | Structured clinical report generation |
| 3 | **ISO 13485** | Medical device quality management |
| 4 | **NeuroKit2** | Neurophysiological signal processing |
| 5 | **PyDicom** | DICOM medical image handling |
| 6 | **PyHealth** | Healthcare ML pipelines |
| 7 | **Treatment Plans** | Treatment planning and protocol design |
</details>
### 📊 Data Science — ML, Statistics & Data Analysis (22 Skills)
<details>
<summary><b>Click to expand full data science skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **Dask** | Parallel computing and out-of-core data |
| 2 | **EDA** | Exploratory data analysis |
| 3 | **NetworkX** | Network/graph analysis |
| 4 | **Polars** | High-performance DataFrames |
| 5 | **PufferLib** | Reinforcement learning environments |
| 6 | **PyMC** | Bayesian statistical modeling |
| 7 | **pymoo** | Multi-objective optimization |
| 8 | **PyTorch Lightning** | Structured deep learning training |
| 9 | **scikit-learn** | Classical machine learning |
| 10 | **scikit-survival** | Survival analysis |
| 11 | **SHAP** | Model interpretability and feature importance |
| 12 | **SimPy** | Discrete-event simulation |
| 13 | **Stable-Baselines3** | Reinforcement learning algorithms |
| 14 | **Statistical Analysis** | Classical statistical tests and methods |
| 15 | **statsmodels** | Statistical models and econometrics |
| 16 | **SymPy** | Symbolic mathematics |
| 17 | **TimesFM** | Foundation model for time series |
| 18 | **PyTorch Geometric** | Graph neural networks |
| 19 | **Transformers** | Hugging Face transformer models |
| 20 | **UMAP** | Dimensionality reduction |
| 21 | **Vaex** | Out-of-core DataFrames for big data |
| 22 | **Zarr** | Chunked, compressed N-dimensional arrays |
</details>
### 📈 Visualization — Scientific Plotting & Graphics (8 Skills)
<details>
<summary><b>Click to expand full visualization skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **Generate Image** | AI image generation for research figures |
| 2 | **Infographics** | Research infographic design |
| 3 | **Matplotlib** | Publication-quality 2D plots |
| 4 | **Mermaid** | Diagrams and flowcharts as code |
| 5 | **Plotly** | Interactive scientific visualizations |
| 6 | **Scientific Schematics** | Technical diagrams and schematics |
| 7 | **Scientific Viz** | Advanced scientific visualization |
| 8 | **Seaborn** | Statistical data visualization |
</details>
### ✍️ Writing Tools — Scientific Writing, Citations & Publishing (13 Skills)
<details>
<summary><b>Click to expand full writing tools skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **Academic Career** | Academic CV, research statements, tenure dossier |
| 2 | **Citation Management** | Reference formatting and management |
| 3 | **Hypothesis Generator** | Research hypothesis development |
| 4 | **LaTeX Posters** | Conference poster design in LaTeX |
| 5 | **Literature Review** | Systematic literature review assistance |
| 6 | **Paper-to-Web** | Convert papers to web-friendly formats |
| 7 | **Peer Review** | Peer review writing assistance |
| 8 | **PPTX Posters** | Conference posters in PowerPoint |
| 9 | **Research Grants** | Grant proposal writing |
| 10 | **Scholar Eval** | Academic output evaluation |
| 11 | **Scientific Slides** | Research presentation creation |
| 12 | **Scientific Writing** | Academic writing style and structure |
| 13 | **Venue Templates** | Journal/conference formatting templates |
</details>
### 🔧 Lab Integrations — Laboratory Platform Connectors (9 Skills)
<details>
<summary><b>Click to expand full lab integration skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **Benchling** | Molecular biology data platform |
| 2 | **DNAnexus** | Genomic data analysis platform |
| 3 | **Ginkgo Cloud** | Synthetic biology platform |
| 4 | **LabArchive** | Electronic lab notebook |
| 5 | **LatchBio** | Bioinformatics workflow platform |
| 6 | **OMERO** | Biological image management |
| 7 | **Opentrons** | Lab automation and robotics |
| 8 | **Protocols.io** | Protocol sharing and management |
| 9 | **PyLabRobot** | Lab robotics programming |
</details>
### 🌍 Domain-Specific — Quantum, Geospatial, Materials, Social Science & More (17 Skills)
<details>
<summary><b>Click to expand full domain-specific skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **Adaptyv** | Adaptive experimental design |
| 2 | **Aeon** | Time series classification |
| 3 | **AstroPy** | Astronomy and astrophysics |
| 4 | **Cirq** | Quantum circuit design (Google) |
| 5 | **FluidSim** | Fluid dynamics simulation |
| 6 | **GeniML** | Genomic interval ML |
| 7 | **GeoMaster** | Geospatial analysis mastery |
| 8 | **GeoPandas** | Geospatial data analysis |
| 9 | **GTARS** | Genomic tool for annotation |
| 10 | **HypoGenic** | Hypothesis generation from data |
| 11 | **Modal** | Cloud compute for research |
| 12 | **PennyLane** | Quantum machine learning |
| 13 | **Pymatgen** | Materials science analysis |
| 14 | **Qiskit** | Quantum computing (IBM) |
| 15 | **QuTiP** | Quantum dynamics simulation |
| 16 | **Social Science Methods** | Discourse analysis, QCA, Delphi, process tracing |
| 17 | **Digital Humanities** | Text mining, corpus linguistics, stylometry, OCR |
</details>
### 📄 Document Tools — Markdown & Document Conversion (2 Skills)
<details>
<summary><b>Click to expand full document tools skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **MarkItDown** | Convert documents to Markdown |
| 2 | **Open Notebook** | Open-format research notebooks |
</details>
### 🔍 Research Tools — Search, Discovery, Methods & Reference Management (14 Skills)
<details>
<summary><b>Click to expand full research tools skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **BGPT Search** | AI-powered research search |
| 2 | **Citation Graph** | Keyless ResearchRabbit analog — citation & co-citation graphs over OpenAlex |
| 3 | **Mixed Methods** | Mixed-methods research design and integration |
| 4 | **Open Science** | Preregistration, FAIR data, open access publishing |
| 5 | **Parallel Web** | Multi-source parallel web search |
| 6 | **PDF Extract** | Elicit-columns analog — per-paper evidence tables from PDFs |
| 7 | **Perplexity** | Perplexity-powered research queries |
| 8 | **PyZotero** | Zotero reference manager integration |
| 9 | **Qualitative Methods** | Thematic analysis, grounded theory, IPA, coding |
| 10 | **Research Ethics** | IRB applications, informed consent, GDPR |
| 11 | **Research Lookup** | Quick research paper discovery |
| 12 | **Scientific Brainstorm** | Structured research ideation |
| 13 | **Scientific Thinking** | Critical scientific reasoning frameworks |
| 14 | **Survey Design** | Questionnaire construction and validation |
</details>
### 💰 Finance & Economics — Financial Data & Analysis (7 Skills)
<details>
<summary><b>Click to expand full finance & economics skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **Alpha Vantage** | Stock and financial market data |
| 2 | **Denario** | Financial data processing |
| 3 | **EDGAR Tools** | SEC filing search and analysis |
| 4 | **FRED** | Federal Reserve economic data |
| 5 | **Hedge Fund Monitor** | Hedge fund tracking and analysis |
| 6 | **Market Research** | Market analysis and intelligence |
| 7 | **US Fiscal Data** | US government fiscal data |
</details>
### 🇹🇷 Turkish Academia — National Platforms & Scholarly Workflow (12 Skills)
<details>
<summary><b>Click to expand full Turkish academia skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **DergiPark** | Harvest metadata, abstracts & PDFs from DergiPark via OAI-PMH |
| 2 | **TR Dizin** | Search TR Dizin & verify a journal's national-index status |
| 3 | **YÖK Tez** | Search the national graduate-thesis archive for review & originality checks |
| 4 | **YÖK Akademik** | Look up a Turkish academic's YÖKSİS profile, title & affiliation |
| 5 | **YÖKATLAS** | Higher-education program & admission statistics (kontenjan, taban puan) |
| 6 | **TÜBİTAK Proposal** | Scaffold TÜBİTAK 1001/1002-A national research proposals |
| 7 | **Doçentlik Eligibility** | Score a publication list against ÜAK associate-professor criteria |
| 8 | **Akademik Teşvik** | Compute the annual academic-incentive (teşvik) score |
| 9 | **TR Academic Style** | Turkish-journal & TR-Dizin formatting + Turkish APA-7 |
| 10 | **TR Research Ethics** | Turkish etik kurul applications & consent-form routing |
| 11 | **KVKK DMP** | KVKK-compliant data-management plans for Turkish research |
| 12 | **Aperta** | TÜBİTAK open-science compliance & deposition into Aperta |
</details>
### 🎓 Faculty Life — Teaching, Service & the Academic Career (6 Skills)
<details>
<summary><b>Click to expand full faculty life skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **Syllabus AI Policy** | Course-level generative-AI use policies & syllabus statements |
| 2 | **Grant Reporting** | Post-award reports — NIH RPPR, NSF, Horizon Europe / ERC |
| 3 | **Recommendation Letters** | Evidence-anchored reference & recommendation letters |
| 4 | **Accreditation (AoL)** | AACSB / ABET assurance-of-learning documentation |
| 5 | **REDCap / CDISC** | Validated data-capture instruments mapped to CDISC standards |
| 6 | **Preprint Deposition** | Deposit preprints to arXiv, bioRxiv, medRxiv, SSRN, OSF |
</details>
### 🧪 Methodology — Research Rigor & Discipline Gates (3 Skills)
<details>
<summary><b>Click to expand full methodology skills list</b></summary>
<br>
| # | Skill | What It Does |
|:---:|:---|:---|
| 1 | **Pre-registration Discipline** | No analysis without a frozen, pre-registered plan |
| 2 | **Test-Selection Guard** | No statistical test chosen after seeing the p-value |
| 3 | **Results Transparency** | No results claim without reporting every analysis run |
</details>
<br>
---
## 🏗️ Project Structure
```
AlterLab-Academic-Skills/
├── 📁 skills/ # 210 skills across 16 domains
│ ├── 🔄 core/ # 8 pipeline + citation-verifier + teaching + thesis skills
│ ├── 🗄️ databases/ # 39 database connectors
│ ├── 🧬 bioinformatics/ # 30 bio/genomics tools
│ ├── ⚗️ cheminformatics/ # 12 chemistry/drug discovery
│ ├── 🏥 clinical-research/ # 7 clinical/medical tools
│ ├── 📊 data-science/ # 22 ML/statistics tools
│ ├── 📈 visualization/ # 8 plotting/charting tools
│ ├── ✍️ writing-tools/ # 13 scientific writing & career tools
│ ├── 🔧 lab-integrations/ # 9 lab platform connectors
│ ├── 🌍 domain-specific/ # 17 specialized field tools
│ ├── 📄 document-tools/ # 2 file format tools
│ ├── 🔍 research-tools/ # 14 search, methods & ethics tools
│ ├── 💰 finance-economics/ # 7 financial/economic tools
│ ├── 🇹🇷 turkish-academia/ # 12 Turkish national-platform & workflow skills
│ ├── 🎓 faculty-life/ # 6 teaching, service & career skills
│ └── 🧪 methodology/ # 3 research-rigor discipline gates
├── 📁 dist/ # per-domain .zip bundles for claude.ai (built on release)
├── 📁 scripts/ # install.sh, gen_catalog.py, run_evals.py, audit_skills.py …
├── 📁 docs/ # evals, integrity & design docs
├── 📄 skills.json # generated machine-readable catalog
├── 📄 README.md # This file
├── 📄 CLAUDE.md # Project instructions
├── 📄 CONTRIBUTING.md # Contribution guidelines
├── 📄 THIRD_PARTY_NOTICES.md # Upstream / K-Dense provenance
└── 📄 LICENSE # MIT License
```
<br>
## ⚙️ How Skills Work
Each `.md` skill file follows a consistent structure:
```markdown
| name | description |
|---------------|-------------------------------------|
| skill-name | When to activate this skill... |
# Skill Title
You are **RoleName**, a [role description]...
## Your Identity & Memory
## Your Core Mission
## Frameworks & Methods
## Output Templates
## Quality Standards
```
> [!NOTE]
> **Pro tip:** Combine multiple skills in one Claude Project for a multi-expert team. For example, load **Deep Research** + **Paper Writer** + **Paper Reviewer** for a complete research-to-publication workflow.
<br>
## 💡 Usage Examples
Skills activate automatically based on user intent:
| You say... | Skill activated |
|:---|:---|
| *"Help me research the latest findings on CRISPR gene editing"* | `alterlab-deep-research` |
| *"Write an academic paper on machine learning in education"* | `alterlab-paper-writer` |
| *"Review my manuscript for methodology issues"* | `alterlab-paper-reviewer` |
| *"Search PubMed for recent studies on Alzheimer's biomarkers"* | `alterlab-pubmed` |
| *"Analyze my RNA-seq data"* | `alterlab-scanpy` + `alterlab-pydeseq2` |
| *"Create a scientific poster for my conference"* | `alterlab-latex-posters` |
| *"Design a survey for my social science study"* | `alterlab-survey-design` |
| *"Help me with my IRB ethics application"* | `alterlab-research-ethics` |
| *"Build a Bayesian model for my clinical trial data"* | `alterlab-pymc` |
| *"Guide my PhD student's thesis writing"* | `alterlab-thesis-supervisor` |
<br>
---
## ⚖️ How It Compares
<div align="center">
*Respectfully, factually — both peers are excellent MIT-licensed projects. This table is about fit, not ranking.*
| | **AlterLab Academic Skills** | **K-Dense scientific-agent-skills** | **anthropics/skills** |
|:---|:---:|:---:|:---:|
| **Skills** | 210 | 138 *(self-reported)* | General-purpose examples |
| **Executable evals** | 210 / 210 shipped; coverage CI-gated, behavioral on demand | Not shipped as an eval harness | Not the project's focus |
| **License** | MIT | MIT | MIT |
| **Academic focus** | Built for the research lifecycle | Scientific tooling | General / reference |
| **Bundles / marketplace** | Per-domain `claude.ai` bundles + Claude Code marketplace | — | — |
</div>
> Counts verified against [`skills.json`](skills.json); K-Dense figure is the upstream project's own self-reported count. `anthropics/skills` is Anthropic's official example collection, scoped to general-purpose demonstrations rather than a fixed academic catalog.
<br>
## 🔗 Sister Projects
- [AlterLab-FC-Skills](https://github.com/AlterLab-IEU/AlterLab-FC-Skills) — 72 agentic skills for communication students
- [AlterLab_GameForge](https://github.com/AlterLab-IEU/AlterLab_GameForge) — 34 game dev skills from concept to launch
## 🤝 Contributing
We welcome contributions! See **[CONTRIBUTING.md](CONTRIBUTING.md)** for guidelines.
**Quick ways to contribute:**
- 🛠️ Improve an existing skill with better frameworks or templates
- ✨ Create a new skill following the structure above
- 🐛 Report issues or suggest improvements
- 📚 Add examples or use cases to documentation
<br>
## 📖 Cite This Repository
If AlterLab Academic Skills supports your research or teaching, please cite it. A machine-readable [`CITATION.cff`](CITATION.cff) ships in the repo, so GitHub's *"Cite this repository"* button and most reference managers can import it automatically. The suite is a content fork of K-Dense's `scientific-agent-skills` (MIT) — see [`THIRD_PARTY_NOTICES.md`](THIRD_PARTY_NOTICES.md) and [`PROVENANCE.md`](PROVENANCE.md) for full provenance.
```bibtex
@software{alterlab_academic_skills_2026,
title = {AlterLab Academic Skills},
author = {{AlterLab Creative Technologies Laboratory, Izmir University of Economics (IEU)}},
year = {2026},
version = {2.1.0},
license = {MIT},
url = {https://github.com/AlterLab-IEU/AlterLab-Academic-Skills}
}
```
<details>
<summary><b>Prefer CFF? Click to expand the <code>CITATION.cff</code> core</b></summary>
```yaml
cff-version: 1.2.0
title: "AlterLab Academic Skills"
type: software
version: 2.1.0
date-released: "2026-06-06"
license: MIT
repository-code: "https://github.com/AlterLab-IEU/AlterLab-Academic-Skills"
authors:
- name: "AlterLab Creative Technologies Laboratory, Izmir University of Economics (IEU)"
website: "https://github.com/AlterLab-IEU"
city: "Izmir"
country: "TR"
```
</details>
<br>
## 📜 License
This project is licensed under the **[MIT License](LICENSE)**.
```
MIT License — Copyright (c) 2026 AlterLab Creative Technologies Laboratory
```
<br>
## 🙏 Credits
<div align="center">
<b>Built with ❤️ by <a href="https://github.com/AlterLab-IEU">AlterLab Creative Technologies Laboratory</a></b>
<br><br>
<b>210 skills · 16 domains · 210 with executable evals · 1 prompt away from expert-level research</b>
<br><br>
<hr>
<sub>If you find this project useful, please consider giving it a ⭐</sub>
<br>
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</div>
<br>
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Information
Repository
Language
Python
Created
2026/6/18
Updated
2026/6/19