single-cell-scrna-seq-analysis-scanpy

What problem does it solve?

Complete end-to-end single-cell RNA-seq analysis workflow using Scanpy and AnnData, enabling researchers to load diverse data formats, perform QC, normalize, reduce dimensionality, cluster cells, and annotate cell types.

Core Features & Use Cases

• Load data from 10X, h5ad, or CSV into an AnnData object.
• QC metrics calculation, filtering, normalization, HVG selection, and visualization.
• Dimensionality reduction (PCA, UMAP/t-SNE) and Leiden clustering across resolutions.
• Marker gene identification and automated/manual cell-type annotation.
• Generate publication-ready plots and trajectories for downstream interpretation.

Quick Start

Load your dataset (10X, h5ad, or CSV) and run the full Scanpy pipeline to obtain QC metrics, clustering, and annotated cell types.