alterlab-scanpy

What problem does it solve?

Streamlines end-to-end single-cell RNA-seq analysis by providing a ready-to-use Scanpy workflow that handles QC, normalization, feature selection, dimensionality reduction, clustering, and annotation, reducing setup time and improving reproducibility.

Core Features & Use Cases

• End-to-end scRNA-seq pipeline including quality control, normalization, HVG selection, PCA/UMAP, Leiden clustering, marker gene identification, and cell-type annotation.
• Trajectory inference with PAGA/dpt and straightforward export of processed data and metadata for downstream reporting.

Quick Start

Run the included template on your scRNA-seq data to execute a full Scanpy workflow from loading to clustering and annotation.