scverse-compact

What problem does it solve?

This Skill provides a compact, end-to-end single-cell RNA-seq analysis workflow using Scanpy on an AnnData object.

Core Features & Use Cases

• QC metrics computation and filtering for cells and genes
• Normalization, log transformation, and highly-variable gene (HVG) selection
• Dimensionality reduction (PCA, UMAP) and neighborhood graph construction
• Clustering (Leiden) and marker gene ranking for identified clusters
• Use Case: Quickly analyze a new scRNA-seq dataset to obtain a ready-to-interpret UMAP map with clusters and marker lists

Quick Start

Use the scverse-compact skill to run a compact single-cell workflow on a given AnnData object, performing QC, filtering, normalization, HVG selection, PCA, neighbors, UMAP, Leiden clustering, and marker gene ranking.