This is the code repository for the manuscript "Re-evaluation and Re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 20%"

This repository contains the code used in the manuscript "Re-evaluation and Re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 20%". The aim of the manuscript and the corresponding code is to describe an approach to iterative re-analysis of Next-Generation Sequencing (NGS) results in rare diseases. The manuscript can be accessed from medRxiv at this link.

Repository Structure

The repository is divided into three subfolders, each holding the scripts and analysis files for different parts of the analysis process:

1. tertiary_analysis: This folder contains the scripts for performing the tertiary analysis of the NGS data.
2. R_analyses: This folder contains the R scripts used for statistical analysis and data visualization.
3. PyMOL_analyses: This folder includes scripts for PyMOL-based protein analyses.

Each folder contains a separate README file with detailed information about the contents and usage of the scripts within.

Getting Started

Before you proceed, ensure you have installed all necessary dependencies. Each script's dependencies are listed at the top of the script.

To clone the repository, run the following command:

git clone https://github.com/berntpopp/conNDD

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use the code in this repository, please cite our manuscript:

Bartolomaeus et al. (2022). Re-evaluation and Re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 20%. medRxiv. https://doi.org/10.1101/2022.10.01.22280361