Spatial Transcriptomics Analysis (Scanpy + Squidpy)

Overview

This project implements an end-to-end pipeline for spatial transcriptomics data analysis using Scanpy and Squidpy.

Features

• Quality control (QC)
• Normalization and log transformation
• PCA, UMAP, Leiden clustering
• Marker gene analysis
• Cell type annotation
• Spatial visualization

Dataset

This project uses a sample Visium dataset provided by Scanpy for demonstration purposes.

Project Structure

src/ # pipeline code results/ # generated figures data/ # input data (not included)

How to Run

python main.py

Output
UMAP plot of clusters
Spatial distribution of cell types