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.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-scgptnpx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-scgpt -a claude-code -gnpx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-scgpt -a codex -ggemini skills install https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git --path skills/bioinformatics/alterlab-scgptgh skill install AlterLab-IEU/AlterLab-Academic-Skills alterlab-scgptgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills /tmp/AlterLab-IEU__AlterLab-Academic-Skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-scgpt ~/.claude/skills/alterlab-scgpt # Claude Code
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-scgpt ~/.agents/skills/alterlab-scgpt # Codex, Cursor, Gemini CLI, Copilot, OpenCode