Stromal_Tcell_Infiltration_mIF

This repository contains preprocessing and analytical scripts associated with the study "Stromal cell subsets modulate T-cell infiltration in early breast cancer".

Key Features

• Data processing and quality control
• Visualization
• Cell colocalisation analysis
• Immune microenvironment analysis

Data Structure

The repository is organized as follows:

• data/: input and processed data files
• scripts/: analysis scripts
• scripts/main_figures.Rmd: main script for figures in the manuscript
• Other scripts in scripts/: preprocessing scripts or specific analysis scripts
• R/: custom utility functions for analysis and visualization
• config/: configuration files for different datasets
• output/: generated outputs, figures, and summary tables
• logs/: run logs

Usage

1. Set config for luminal and TNBC datasets in config/. In the analysis scripts, you can choose different config files for luminal and TNBC datasets to run the workflow for each cohort.
2. Run main_figures.Rmd for main figure plotting and integrated analysis.
3. Run specific analysis scripts in scripts/ for focused analyses.

Data Availability

The data generated in this study are available in the supplementary files or from the corresponding author upon reasonable request.

Contacts

All other relevant data and analysis are available from the authors upon request. For further enquires, please raise an issue via GitHub or email Hanyun Zhang (Lead author - h.zhang@garvan.org.au), Julia Chen (Lead author - j.chen@garvan.org.au), or Alexander Swarbrick (Lab Head - a.swarbrick@garvan.org.au).