Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
Install
npx skills add K-Dense-AI/scientific-agent-skills --skill scanpynpx skills add K-Dense-AI/scientific-agent-skills --skill scanpy -a claude-code -gnpx skills add K-Dense-AI/scientific-agent-skills --skill scanpy -a codex -ggemini skills install https://github.com/K-Dense-AI/scientific-agent-skills.git --path scientific-skills/scanpygh skill install K-Dense-AI/scientific-agent-skills scanpygit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills /tmp/K-Dense-AI__scientific-agent-skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/K-Dense-AI__scientific-agent-skills/scientific-skills/scanpy ~/.claude/skills/scanpy # Claude Code
cp -R /tmp/K-Dense-AI__scientific-agent-skills/scientific-skills/scanpy ~/.agents/skills/scanpy # Codex, Cursor, Gemini CLI, Copilot, OpenCode