The role of IgE patterns and their link to the gut microbiome in allergic sensitization

This repository contains the analysis code, notebooks, and figures for the study of IgE patterns and their association with the gut microbiome in allergic sensitization.

Repository Structure

• notebooks/: Jupyter notebooks and R Markdown for all analyses
  • 01_IgE_analysis.ipynb: IgE data analysis and workflow
  • 02_diversity.ipynb: Microbiome diversity analysis
  • 03_DA_analysis.ipynb: Differential abundance analysis
  • 04_classification.ipynb: Classification modeling
  • 05_Network_analysis.ipynb: Microbial network analysis
  • 06_Network_visualization.Rmd: Network visualization (R Markdown)
• figures/: Key figures and visualizations
  • abstract.png: Visual abstract (see above)
  • cooccurrence_heatmap.png, ige_expression_boxplot.png, LAC_cube.png, presence_absence_heatmap.png, scree_plot.png: Analysis figures
• requirements.txt: Python dependencies
• Dockerfile: Reproducible environment setup

How to Reproduce

1. Clone the repository
2. Set up the environment
   • Use the provided Docker image for a fully reproducible environment:
     • Pull the image: docker pull ovlasovets/rpy2:latest
     • Start a container (mounting your repo):

        docker run -it --rm -p 8888:8888 -v $(pwd):/workspace ovlasovets/rpy2:latest

     • Launch Jupyter inside the container as instructed, or follow the container's README for details.
   • Alternatively, install Python dependencies from requirements.txt:

      pip install -r requirements.txt

3. Run the notebooks
   • Open the notebooks in the notebooks/ directory and follow the instructions in each notebook.

License

MIT License

Contact

For questions, contact oleg.vlasovets@helmholtz-munich.de.