TOTKA is a comprehensive R-Shiny application for integrated AOP‑anchored framework that combines transcriptomic dose-response modeling with physiologically based kinetic (PBK) simulation.
It integrates following core R packages into a single graphical interface, enabling streamlined physiologically based kinetic (PBK) simulation and adverse outcome pathway (AOP) mapping:
AOPfingerprint APIs are also hosted here
- TOTKA is also available as a docker at docker hub
How to use:
docker pull fhaive/totka:latest
docker run -p 80:80 totka:latest /bin/bash -c "cd /TOTKA/ && R -e \" options('shiny.port'=80,shiny.host='0.0.0.0');library(TOTKA);setwd('/TOTKA/');TOTKA::run_app() \""
Open your browser and visit: 127.0.0.1:80
- AOPFingerprint APIs are also available as a docker at docker hub
You can try out TOTKA immediately with the demo dataset included in the repository under the sample_data/liver_spheroids/ folder.
This is omics data generated from PFOS and PFOA exposure in in-vitro liver spheroids across multiple dose levels and four time points (1, 4, 10 and 14 day) (Rowan-Carroll et al., 2021). Click here for the original article describing the dataset
remotes::install_github("https://github.com/fhaive/totka")
library(TOTKA)
TOTKA::run_app().
├── data/ # Data used by the app
├── sample_data/ # Sample data to run the app
├── PIPELINE_SCRIPT/ # Scripts to execute the analysis pipeline
├── manual/ # Documentation or user guides
├── server.R # Main Shiny server function
└── ui.R # Main Shiny UI definition
- This app provides a user-friendly interface for navigating integrated OMICS and PBK analysis outputs.
- Assessment in the context of Adverse Outcome Pathway (AOP).
- R ≥ 4.0
- R packages are managed via
renv(seerenv.lock)
For questions, suggestions, or contributions, please contact [Angela Serra] at [angela.serra@tuni.fi].