Group 3

Input we need

• Sample metadata (Group 1)
• Run metadata (Group 1)
• Taxonomy data (Group 2B)

Output we will create

We are building a Shiny app with the following tabs:

• Data Upload & Overview: users upload microbiome and metadata files and see a summary: how many patients and controls there are, and what taxa are included. A key feature is the ability to filter all analyses to a single patient, allowing personalized exploration throughout the app. Uploaded data is validated, and tables are displayed for quick checks.
• Taxonomic Composition: this tab explores which microbes are present and how their abundance differs between patients and controls, or across specific diseases or individual patients. Users can apply statistical tests to identify differentially abundant taxa, and visualize clustering patterns to see how similar or different samples are.patients are from each other.
• Diversity Analysis: focuses on microbiome diversity within and between samples. Alpha diversity is assessed using metrics like Shannon and Simpson indexes, while beta diversity is visualized with PCoA or NMDS plots.
• Clinical & Lifestyle Correlations: links microbiome features with clinical and lifestyle factors, such as health status, BMI, exercise, and diet. Users can visualize correlations and explore statistically significant associations through interactive plots.
• Pipeline Summary & Reports: summarizes the entire analysis: run settings, metadata, key findings, and software versions. Users can download detailed reports in PDF, HTML, or Excel, including figures and tables for sharing or documentation.

Objectives of the group

Our group is focused on making microbiome results easy to understand and useful for clinicians. We will create clear and interactive visualizations, like charts, graphs, and tables, that help make sense of complex data. We will also prepare simple, well-organized reports that non-technical users can follow. By working closely with the pipeline team, we will make sure everything is properly formatted and ready for delivery. Finally, we will build an intuitive dashboard so users can easily explore the data and find the information they need.

Progress of the group

Documentation of the functions

Function 1 example code in python or R