Multimodal_breast_cancer_subtype_analysis

Profiling intratumoural heterogeneity of breast cancer subtypes through integrated transcriptomic and metabolic analysis at single-cell and spatial resolution

Requirements

Install Pytorch and pytorch-geometric

Install POT: Python Optimal Transport

conda install -c conda-forge pot

Install SpatialMST package for spatial multimodal integration

PyPI package: https://pypi.org/project/SpatialMST

pip install SpatialMST
pip install scanpy

Generate metabolic flux rates and metabolite abundances for single-cell and spatial transcriptomics using scFEA.

https://www.biorxiv.org/content/10.1101/2020.09.23.310656v1.full https://github.com/changwn/scFEA/tree/master

Download the breast cancer single_cell and spatial transcriptomics datasets from figshare

Dataset