📦 BMDx2 Shiny Application

BMDx2 is a comprehensive R-Shiny application for dose-dependent analysis of toxicogenomic data.

It integrates three core R packages into a single graphical interface, enabling streamlined dose–response modeling, pathway enrichment, and adverse outcome pathway (AOP) mapping:

• BMDx package
• AOPfingerprintR package
• FunMappOne package

BMDx APIs are also hosted here
AOPfingerprint APIs are also hosted here

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Docker

• BMDx2 is also available as a docker at docker hub

How to use:

docker pull fhaive/bmdx2:latest
mkdir -p GLP_logs
docker run --rm -it -p 3838:3838 -v ./GLP_logs/:/srv/shiny-server/bmdx2/GLP_logs fhaive/bmdx2:latest

• AOPFingerprint APIs are also available as a docker at docker hub
• BMDx APIs are also available as a docker at docker hub

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🚀 Quick Start (Demo)

You can try out BMDx2 immediately with the demo dataset included in the repository under the bleomycin_data folder.

This is a transcriptomics dataset comprises RNA-Seq data from bleomycin exposure at six doses (0, 20, 40, 60, 80, 100 µg/mL) and three time points (24, 48, and 72 hours). Click here for the original article describing the dataset

Launch the app locally

source("run_app_local.R")

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📁 Folder Structure

.
├── data/                         # Data used by the app
├── manual/                       # Documentation or user guides
├── renv/                         # R environment management (package cache)
├── renv.lock                     # Locked dependencies for reproducibility
├── report.Rmd                    # R Markdown report for results summarization
├── run_app_local.R               # Script to launch the app (entry point)
├── server_modules/               # Modular server-side logic (Shiny modules)
├── server.R                      # Main Shiny server function
├── ui_functions/                 # Custom UI components used in the app
├── ui.R                          # Main Shiny UI definition
└── www/                          # Static resources (images, CSS, JavaScript)

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📑 Description

• This app provides a user-friendly interface for navigating BMD analysis outputs.
• Modular architecture using server_modules/ and ui_functions/ supports reusability.
• Includes markdown-based reporting (report.Rmd) and embedded static assets (www/).

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📦 Requirements

• R ≥ 4.0
• R packages are managed via renv (see renv.lock)

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📬 Contact

For questions, suggestions, or contributions, please contact [Angela Serra] at [angela.serra@tuni.fi].