AlterLab-Academic-Skills

📋 Table of Contents

Click to expand / collapse

• 🎯 What Is This?
• ✨ Key Features
• 🗂️ Domain Overview
• 🚀 Quick Start
• ⚡ Core Pipeline — 7 Skills
• 📚 All 180 Skills
• 🏗️ Project Structure
• ⚙️ How Skills Work
• 💡 Usage Examples
• 🤝 Contributing
• 📜 License
• 🙏 Credits

🎯 What Is This?

A comprehensive suite of 180 purpose-built Claude AI skills for faculty members, academicians, and researchers — organized into 13 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.

✨ 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	7	Multi-agent research → write → review → publish pipeline + teaching + thesis
🗄️	Databases	39	Connectors to scientific databases — PubMed, ChEMBL, UniProt, ClinicalTrials.gov, COSMIC, and more
🧬	Bioinformatics	25	Genomics, proteomics, molecular biology — Scanpy, BioPython, ESM, single-cell analysis
⚗️	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	12	Search, discovery, Zotero, qualitative methods, ethics, surveys, open science
💰	Finance & Economics	7	FRED, Alpha Vantage, SEC EDGAR, market research

🚀 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.

📁 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/<name>/SKILL.md or .claude/skills/<name>/SKILL.md — a bare git clone alone does not register anything.

🌐 Option 4 — Claude.ai

Zip a skill directory and upload it under Settings → Capabilities (requires a plan with code execution). Skills do not sync between claude.ai and Claude Code.

---

⚡ Core Pipeline — 7 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	🎓 Teaching Design	—	Course design, syllabi, rubrics, Bloom's taxonomy, backward design
6	📋 Thesis Supervisor	—	Dissertation guidance, defense prep, committee management
7	🔗 Link Health	—	Repo link-health audit meta-skill

---

📚 All 180 Skills

🗄️ Databases — Scientific Database Connectors (39 Skills)

Click to expand full database skills list

#	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

🧬 Bioinformatics — Genomics, Proteomics & Molecular Biology (25 Skills)

Click to expand full bioinformatics skills list

#	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

⚗️ Cheminformatics — Chemistry & Drug Discovery (12 Skills)

Click to expand full cheminformatics skills list

#	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

🏥 Clinical Research — Clinical Decision Support & Medical Tools (7 Skills)

Click to expand full clinical research skills list

#	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

📊 Data Science — ML, Statistics & Data Analysis (22 Skills)

Click to expand full data science skills list

#	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

📈 Visualization — Scientific Plotting & Graphics (8 Skills)

Click to expand full visualization skills list

#	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

✍️ Writing Tools — Scientific Writing, Citations & Publishing (13 Skills)

Click to expand full writing tools skills list

#	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

🔧 Lab Integrations — Laboratory Platform Connectors (9 Skills)

Click to expand full lab integration skills list

#	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

🌍 Domain-Specific — Quantum, Geospatial, Materials, Social Science & More (17 Skills)

Click to expand full domain-specific skills list

#	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

📄 Document Tools — Markdown & Document Conversion (2 Skills)

Click to expand full document tools skills list

#	Skill	What It Does
1	MarkItDown	Convert documents to Markdown
2	Open Notebook	Open-format research notebooks

🔍 Research Tools — Search, Discovery, Methods & Reference Management (12 Skills)

Click to expand full research tools skills list

#	Skill	What It Does
1	BGPT Search	AI-powered research search
2	Mixed Methods	Mixed-methods research design and integration
3	Open Science	Preregistration, FAIR data, open access publishing
4	Parallel Web	Multi-source parallel web search
5	Perplexity	Perplexity-powered research queries
6	PyZotero	Zotero reference manager integration
7	Qualitative Methods	Thematic analysis, grounded theory, IPA, coding
8	Research Ethics	IRB applications, informed consent, GDPR
9	Research Lookup	Quick research paper discovery
10	Scientific Brainstorm	Structured research ideation
11	Scientific Thinking	Critical scientific reasoning frameworks
12	Survey Design	Questionnaire construction and validation

💰 Finance & Economics — Financial Data & Analysis (7 Skills)

Click to expand full finance & economics skills list

#	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

---

🏗️ Project Structure

AlterLab-Academic-Skills/
├── 📁 skills/
│   ├── 🔄 core/                # 6 pipeline + teaching + thesis skills
│   ├── 🗄️ databases/           # 39 database connectors
│   ├── 🧬 bioinformatics/      # 25 bio/genomics tools
│   ├── ⚗️ cheminformatics/     # 12 chemistry/drug discovery
│   ├── 🏥 clinical-research/   # 10 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/      # 6 file format tools
│   ├── 🔍 research-tools/      # 12 search, methods & ethics tools
│   └── 💰 finance-economics/   # 7 financial/economic tools
├── 📁 .claude/
│   └── CLAUDE.md               # Project-level Claude config
├── 📄 README.md                # This file
├── 📄 CLAUDE.md                # Project instructions
├── 📄 CONTRIBUTING.md          # Contribution guidelines
└── 📄 LICENSE                  # MIT License

⚙️ How Skills Work

Each .md skill file follows a consistent structure:

| 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.

💡 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

---

🔗 Sister Projects

• AlterLab-FC-Skills — 72 agentic skills for communication students
• AlterLab_GameForge — 34 game dev skills from concept to launch

🤝 Contributing

We welcome contributions! See 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

📜 License

This project is licensed under the MIT License.

MIT License — Copyright (c) 2026 AlterLab Creative Technologies Laboratory

🙏 Credits