CADD Threshold APP

This web application investigates the score distribution of known pathogenic and bening variants for different CADD PHRED-score thresholds. The app was built with Shiny for Python and provides a framework for loading, processing and visualising data.

This repository contains a Shiny-for-Python web application that analyzes the distribution of ClinVar variants across different CADD PHRED-score thresholds and provides interactive visualizations and per-gene filtering.

This README explains how to set up, run and develop the application locally.

Features

• Load preprocessed ClinVar + CADD annotation tables for multiple versions and genome builds
• Compare score distributions across versions and genome releases
• Filter the dataset by gene lists (paste or upload) and compute metrics across thresholds
• Export filtered annotations and view per-gene summaries

Requirements

• Python 3.10+ (3.12 recommended)
• See requirements.txt or environment.yml for the full dependency list

Quick setup (pip)

1. Clone the repo:

git clone https://github.com/kircherlab/CADD_threshold_app.git
cd CADD_threshold_app

2. Install dependencies:

pip install -r requirements.txt

Alternatively, use Conda with the provided environment.yml:

conda env create -f environment.yml -n CADD_threshold_app
conda activate CADD_threshold_app

Run the app locally

From the repository root:

python -m shiny run --port 8080 --host 0.0.0.0 app.py

Open http://localhost:8080 in your browser.

Development notes

• The app entry point is app.py and server logic is implemented in server_logic.py.
• Data loading helpers are in data_loader.py.
• Gene parsing and small utilities are in modules/functions_server_helpers.py and modules/read_genes_from_list_or_file_functions.py.
• Plot factories live under modules/ (e.g. basic_plot.py, basic_bar_plot.py).

Project structure (high level)

• app.py - Shiny app entrypoint
• server_logic.py - reactive handlers and UI wiring
• modules/ - plotting helpers, parsing utilities and helper modules
• data/ - data files (not all may be tracked in repo)
• markdowns/ - documentation and page texts used in the app
• requirements.txt, environment.yml - dependency manifests

Contact / License

• See LICENSE in the repository for licensing information.
• For questions about the dataset and analysis, contact the repository maintainers.