Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-scanpynpx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-scanpy -a claude-code -gnpx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-scanpy -a codex -ggemini skills install https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git --path skills/bioinformatics/alterlab-scanpygh skill install AlterLab-IEU/AlterLab-Academic-Skills alterlab-scanpygit 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-scanpy ~/.claude/skills/alterlab-scanpy # Claude Code
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-scanpy ~/.agents/skills/alterlab-scanpy # Codex, Cursor, Gemini CLI, Copilot, OpenCode