Alterlab Scgpt Agent Skill
Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.
Install
one command, takes just this skill from the repositorynpx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-scgptOther skills for the same job
different authors, same section of the catalogue
Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, engineering, math, drug discovery, protein design, weather modeling, theorem proving, single-cell, or PDE solving. Hugging Science is a curated catalog of scientific datasets, models, blog posts, and interactive Spaces. This skill helps discover and use resources via `datasets`, `transformers`, the HF Inference API, `gradio_client`, and methodology citations.
Publish and manage research papers on Hugging Face Hub. Supports creating paper pages, linking papers to models/datasets, claiming authorship, and generating professional markdown-based research articles.
Semantic search, similar content discovery, and structured research using Exa API. Use when you need semantic/embeddings-based search, finding similar content, or searching by category (company, people, research papers, etc.).
Build RAG (Retrieval Augmented Generation) pipelines with web search and LLMs. Tools: Tavily Search, Exa Search, Exa Answer, Claude, GPT-4, Gemini via OpenRouter. Capabilities: research, fact-checking, grounded responses, knowledge retrieval. Use for: AI agents, research assistants, fact-checkers, knowledge bases. Triggers: rag, retrieval augmented generation, grounded ai, search and answer, research agent, fact checking, knowledge retrieval, ai research, search + llm, web grounded, perplexity alternative, ai with sources, citation, research pipeline
| Build RAG (Retrieval Augmented Generation) pipelines with web search and LLMs. research agent, fact checking, knowledge retrieval, ai research, search + llm, web grounded, perplexity alternative, ai with sources, citation, research pipeline
Web search and content extraction with Tavily and Exa via inference.sh CLI. Apps: Tavily Search, Tavily Extract, Exa Search, Exa Answer, Exa Extract. Capabilities: AI-powered search, content extraction, direct answers, research. Use for: research, RAG pipelines, fact-checking, content aggregation, agents. Triggers: web search, tavily, exa, search api, content extraction, research, internet search, ai search, search assistant, web scraping, rag, perplexity alternative
Web search and content extraction with Tavily and Exa via inference.sh CLI. Apps: Tavily Search, Tavily Extract, Exa Search, Exa Answer, Exa Extract. Capabilities: AI-powered search, content extraction, direct answers, research. Use for: research, RAG pipelines, fact-checking, content aggregation, agents. Triggers: web search, tavily, exa, search api, content extraction, research, internet search, ai search, search assistant, web scraping, rag, perplexity alternative
The protocol behind every investigation skill. Use when AI research must proceed without you: search-plan gate, Fact/Inference/Assumption labels, confidence stacking, diffable outputs.
How to use it
Take alterlab-ieu/alterlab-scgpt from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.