OmniMeta 🧬

OmniMeta is a robust and user-friendly R Shiny application designed as the official downstream analysis tool for the PEMS-Pipeline. It bridges the gap between raw taxonomic profiles and biological insights, allowing researchers to perform complex statistical analyses without writing a single line of code.

Designed specifically for Bracken/Kraken2 outputs, OmniMeta integrates powerful R packages like phyloseq, DESeq2, and vegan into an intuitive Graphical User Interface (GUI).

🚀 Key Features

• Automated Setup: The script automatically detects and installs all necessary CRAN and Bioconductor dependencies upon the first run.
• Multi-Level Taxonomy: Automatically aggregates and analyzes data across all taxonomic ranks (Domain to Species).
• Comprehensive Workflow:
  • QC & Rarefaction: Good's Coverage and Rarefaction curves.
  • Alpha Diversity: Multiple indices (Shannon, Simpson, Chao1, ACE, Pielou) with Kruskal-Wallis stats.
  • Beta Diversity: PCoA (Bray-Curtis) with PERMANOVA statistical testing.
  • Relative Abundance: Dynamic bar plots with "Top N" filtering.
  • Differential Abundance: Automated DESeq2 pipeline supporting multi-group comparisons.
  • Core Microbiome: Heatmaps with customizable prevalence and abundance thresholds.
  • Co-occurrence Networks: Network construction using Spearman correlation.
• Auto-Save: Automatically exports high-resolution figures (TIFF 600dpi) and statistical tables (TSV) to a local directory.

🛠️ Requirements

• R (version 4.0 or higher)
• RStudio (optional, but recommended for launching)
• Input Data:
  • Abundance: A folder containing .txt output files from Bracken.
  • Metadata: A .tsv file containing sample information (must match filenames).

📦 How to Run

1. Clone or download this repository.
2. Open app.R in RStudio.
3. Click the "Run App" button.
4. Note: On the first launch, the app will automatically install all required packages. This may take a few minutes.

📊 Usage

1. Upload: Select the folder containing your Bracken files and upload your metadata file.
2. Configuration: Define your grouping column (e.g., "Treatment") and control group (e.g., "Control").
3. Select Analyses: Check the boxes for the specific pipelines you wish to run.
4. Run: Click "RUN ANALYSIS & AUTO-SAVE". Results will be saved directly to your selected output folder.

📄 Citation

If you use OmniMeta in your research, please cite it as:

Oliveira, A. F. B. (2025). OmniMeta: Automated R Shiny Pipeline for Shotgun Metagenomics. GitHub. https://github.com/oliv-angelus/OmniMeta. DOI: 10.5281/ZENODO.17842149

👤 Author

• Angelo Felipe Barbosa de Oliveira
• Lattes: http://lattes.cnpq.br/5450775990055106
• ORCID: https://orcid.org/0000-0003-0831-447X

⚖️ License

This project is licensed under the MIT License. See the LICENSE file for details.