📦 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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Data folder

The data folder can be found at: 10.5281/zenodo.17366287 The data folder is needed to run the BMDx2 app when executed from RShiny. The data folder should be placed in the main folder of the BMDx2 app at the same level of the ui.R and server.R files.

📑 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].