Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h5ad. Applies to established exploratory scRNA-seq workflows with explicit count and expression provenance; complementary skills cover scvi-tools models and AnnData format details.
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 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/skills/scanpy ~/.claude/skills/scanpy # Claude Code
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/scanpy ~/.agents/skills/scanpy # Codex, Cursor, Gemini CLI, Copilot, OpenCode