scanpy

Features and purpose

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.

Quick start

Follow the repository instructions for this skill and your agent. Review the files and dependencies before adding it to your workflow.