Welcome to spMetaTME’s documentation!

spMetaTME spMetaTME: A spatial atlas of tumour microenvironment metabolism and interactions

Unlike traditional flux estimation approaches, spMetaTME represents the metabolic network as a directed hypergraph, where metabolites are represented as nodes and reactions as hyperedges, enabling the modelling of directional reactant-to-product flux propagation. By leveraging self-supervised hypergraph learning, spMetaTME captures the intrinsic metabolic dependencies and directional flux propagation across spatially adjacent cells or spots.

Contents:

• Installation
  • Prerequisites
  • Standard Installation
  • Installing from Source
  • Verifying Installation
  • Troubleshooting
• Docker Tutorial
  • Prerequisites
  • Building the Image
  • Basic Usage
  • Working with Local Data
  • Windows Helper: run_docker.cmd
  • Advanced: Accessing the Container Shell
• CLI Usage Guide
  • Getting Help
  • 1. Metabolic Inference (spmetatme infer)
  • 2. Base Model Pretraining (spmetatme pretrain)
  • Tip: Available Metabolic Models
• Estimate Spatial Metabolic fluxes
  • Overview
  • Dataset Information
  • Import Required Libraries
  • Explore Available Metabolic Models
  • Load and Preprocess Spatial Transcriptomics Data
  • Load Tissue-Specific Metabolic Model
  • Construct Metabolic Data Loader
  • Infer Metabolic Fluxes and Identify Spatial Metabolic Domains
  • spatial distribution of spatial metabolic domains
  • Infer Metabolic Interactions Between Spatial Regions
• Metabolic Domains and Fluxes Analysis
  • Load Spatial metabolic fluxes
  • Compute and Visualize UMAP Embeddings
  • Metabolite distribution of reaction fluxes across domains
  • Spatial map view of reactions in “Glycolysis / Gluconeogenesis” pathway
  • Spatial map view of reactions in Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism pathway
  • Spatial map view of reactions in Exchange/demand reactions pathway
  • Investigate the spatial fluxes for exchange reactions differentially enriched in domain 1.
  • Domain-Specific Differentially Enriched Reactions
  • Investigate Glycolysis/Gluconeogenesis Pathway
  • Investigate Exchange/demand reactions Pathway
  • Investigate differentially enriched top 15 pathways
  • Investigate top 20 Pathways by variance
• Metabolic interactions in the tumor microenvironment
  • Load Spatial metabolic fluxes
  • Visualise the distribution of Interaction Types
  • Tissue-level Metabolic Interaction Types for selected exchange reactions
  • Domain-wise Metabolic Interaction Types for selected exchange reactions
  • Investigate the metabolic interaction types of top n (n = 2) exchange reactions differentially enriched in each domain.
  • Quantify Metabolic Communication in the Tissue
• Spatial Metabolite Analysis
  • Load Spatial metabolic fluxes
  • Spatial Maps of Metabolites
  • Plot spatial metabolite distribution by metabolite id
  • Metabolite distribution across compartments and domains
  • Identify differentially enriched metabolites

Indices and tables

• Index

• Module Index

• Search Page

Please cite

• Verma, S., Doan, L. M. T., Kang, J. H., Colombo, G., Serganov, I., Zappasodi, R., Occhipinti, A., & Angione, C. spMetaTME: A spatial atlas of tumour microenvironment metabolism and interactions.