Nephro Candidate Score - a tool for automatic prioritization of variants in kidney disease patients

Welcome to the GitHub repository "Nephro Candidate Score". The Nephro Candidate Score (NCS) is a tool for standardized and automatic prioritization of candidate variants in kidney disease patients. It integrates information from multiple open-source databases and scores variants based on a machine learning algorithm.

Table of contents

• Overview and Methods
• Usage
• File structure
• License
• Creators
• Contact

Overview and Methods

TODO

Usage

The NCS is publicly available and accessible. A web tool version for single variant scoring is available on TBA. A command line tool for scoring .vcf files is available on TBA.

File Structure

The repository has the following structure:

.
├── gene_score/
│   ├── features/
│   │   ├── raw/
│   │   ├── results/
│   │   ├── scripts/
│   │   │   ├── cellxgene.R
│   │   │   ├── descartes.R
│   │   │   ├── exon_CpG_o2e_ratio.R
│   │   │   ├── exon_and_prom_conservation.R
│   │   │   ├── gnomad.R
│   │   │   ├── gtex.R
│   │   │   ├── kidney_network.R
│   │   │   ├── mgi_mpo.R
│   │   │   ├── nephrogenesis_atlas.R
│   │   │   ├── paralogues.R
│   │   │   ├── promoter_CpG_o2e_ratio.R
│   │   ├── helper_functions.R
│   ├── labels/
│   │   ├── raw/
│   │   ├── results/
│   │   ├── scripts/
│   │   │   ├── dispensable_genes.R
│   │   │   ├── positive_genes.R
│   ├── raw/
│   ├── training/
│   ├── gene_score_preprocessing_master.R
│   ├── helper_functions.R
│   ├── hgnc_functions.R
└── variant_score/

• The gene_score/ directory contains all scripts relevant for data acquisition and machine learning development of the gene score. Due to large file sizes, the raw data is not completely stored on GitHub.
• The variant_score/ TBA

License

This project is licensed under the terms of the MIT license. For more information, please refer to the License TBA file.

Creators and contributors

Nina Rank

• https://github.com/ninarank
• https://orcid.org/0000-0002-5984-4836

Bernt Popp

• https://twitter.com/berntpopp
• https://github.com/berntpopp
• https://orcid.org/0000-0002-3679-1081
• https://scholar.google.com/citations?user=Uvhu3t0AAAAJ

Soeren Lukassen

• https://github.com/slukassen
• https://orcid.org/0000-0001-7045-6327
• https://scholar.google.com/citations?user=wWiHGZkAAAAJ&hl=en

Constantin Aaron Wolff

• https://github.com/ConstantinWolff
• https://orcid.org/0000-0002-3277-4559

Jan Halbritter

• https://orcid.org/0000-0002-1377-9880
• https://scholar.google.com/citations?user=Jt1S5fkAAAAJ

Contact

If you have any questions, suggestions, or feedback, please feel free to contact [email protected].