README.md

MicroLoop: A shiny R app for Metagenomics data analysis

Microbiome data analysis has posed many challenges on the researchers and decision-making entities, due to its complexity and hefty work that comes with it. In addition, due to lack of a golden standard for this type of sparce data analysis reproducibility of the results from lab to lab might be jeopardized. Therefore, MicroLoop was developed as a shiny app in R to perfom a wide variety of task with no need for hard-coding and any demanding bioinformatics skills.

The app offers modules for the following analysis:

1. Reading a variety of data formats

2. Basic inferences on the data

3. Preprocessing and cleaning up the data

4. Mixed-model complex statistical analysis on within sample variance (Alpha diversity)

5. Data normalization and multivariate analysis of variance between groups (Beta diversity)

6. Creating stacked bar plot on the distribution of different taxa across different variables (groups/samples)

7. Differential abundance analysis with multiple known tools

8. Association/correlation analysis between numerical variables and mcirbtiome data

9. Phylogenetic-based analysis and tree visualizations

In all these stages you can download modified dataset, generated tables and high-resolution publication-ready plots!

This app is hosted on an ECS inctance on Amazon Web Service (AWS)

---