Spatial Transcriptomics Analysis of Breast Cancer

Overview

This project investigates immune exclusion and ECM remodelling using Visium and Xenium datasets.

Contents

• 01.Visium_RCTD.R: segmentation and deconvolution of visium data
• 02.Visium_Anlysis.R: clustering, communication analysis and function enrichment
• 03.Xenium_RCTD.R: segmentation and deconvolution of xenium data
• 04.Xenium_5k_BC.R: processing, clustering and marker gene selection

Methods

• Clustering (Seurat)(BANKSY)
• Cell-cell communication (CellChat)
• Find marker genes(Seurat)
• GO enrichment (gprofiler2)

How to run

1. Load data
2. Run scripts in order

Data source

Public datasets from 10x Genomics

Visium:Visium_HD_FF_Human_Breast_Cancer - Gene expression library of Fresh Frozen Human Breast Cancer (Visium HD) using the Human Whole Transcriptome Probe Set

Xenium:FFPE Human Breast Cancer with 5K Human Pan Tissue and Pathways Panel plus 100 Custom Genes

Notes:

• Data not included due to size; sourced from 10X Genomics Public Datasets