STged Tutorial and Example Guide []

This tutorial provides a comprehensive guide on using STged with toy examples, covering both simulation and real data analyses.

Data Source

The simulation data, real data, and results from both STged and compared methods in this study are available on the Zenodo website: .

Key Fixes:

1. Replaced "compated methods" with "compared methods."
2. Improved phrasing for readability and grammatical correctness.
3. Fixed the link syntax by ensuring it redirects correctly.

File Structure and Contents

The following folders contain all necessary code, data, and documentation to reproduce main and supplementary results in the STged study:

1. Code Folder:

• Benchmark File: Contains code for implementing benchmark methods used for comparison with STged.
• Module File: Contains code for STged-specific modules designed for analyzing real data.
• Figures Code: Includes scripts for generating figures from STged analyses.

2. Simulation Folder:

• Contains both code and demo files needed to reproduce results for main and supplementary STged simulation studies, enabling a full demonstration of STged's simulation-based performance.

3. Demo Folder:

• Contains code and demo files for reproducing STged results in real data analyses, specifically tailored to the examples used in the main and supplementary results sections.

Tutorials

Detailed tutorials provide step-by-step guidance on running analyses on simulated and real data.

Simulation Studies

These tutorials demonstrate STged’s functionality on simulated datasets, providing insight into its performance in controlled settings.

• seqFISH+ Data Analysis: A demo showcasing STged applied to seqFISH+ data simulations.
• MERFISH Data Analysis: A tutorial on applying STged to MERFISH simulated data.

Real Data Studies

Real data examples illustrate STged’s capabilities in practical applications, focusing on human PDAC tissue and mouse kidney tissue.

• mHVG/ctHVG Module Analysis: Analyzing mHVG and ctHVG in human PDAC tissue, focusing on identifying highly variable genes linked to cell types.
• Cell Type Subpopulation Analysis: Identifying and analyzing cell subpopulations within human PDAC tissue.
• Cell-Cell Communication Analysis: Analyzing cell-cell communication dynamics in human PDAC tissue.
• Gene Expression Program Module: Gene expression analysis of mouse kidney tissue, showcasing spatial gene expression programs.