An R Shiny web application to explore the chicken gut microbiome and their genetic makeup.
chickMicro is an interactive web application for analysing poultry gut microbiome metagenomic data, with a focus on antimicrobial resistance (AMR) profiling. It processes outputs from Abricate (gene detection) and Kraken2/Bracken (taxonomic classification).
- 📂 Upload and parse CSV files generated from metagenomic pipelines
- 🔍 Filter data by database (CARD, VFDB, PlasmidFinder), coverage %, identity %, and gene/taxa count thresholds
- 📊 Visualise AMR gene profiles and multidrug resistance (MDR) patterns across samples
- 📋 Explore summary statistics in interactive tables
- 📄 Generate downloadable HTML reports from filtered data
The dataset comprises broiler chicken gut samples across three dietary treatment groups: Reference diet, Soyabean meal, and Seaweed.
# From R or RStudio, set working directory to the app folder:
setwd("chickMicro/app")
shiny::runApp()Or open chickMicro/app/ui.R in RStudio and click Run App.
👤 Julio C. Ortega Cambara
🎓 PhD Candidate — Computational Bioinformatics
🏛️ School of Biomedical Sciences, University of West London
📍 St Mary's Rd, London W5 5RF
✉️ Email: 32104617@student.uwl.ac.uk