scanpy

SUMMARY

What it does

This Agent Skill provides a standard single-cell RNA-seq analysis pipeline using Scanpy, covering quality control, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and conversion of R-friendly single-cell formats (Seurat or SingleCellExperiment RDS files) to h5ad. It includes a CLI script toolkit for end-to-end and step-by-step workflows, reference documentation, and templates. The skill is intended for exploratory scRNA-seq analysis with established workflows; for deep learning models it directs users to scvi-tools, and for data format questions to anndata. The source was inspected and found to be a Markdown file with 321 lines, including installation instructions, usage guidance, and references.