Welcome to the GitHub repository "Kidney-Genetics", a systematically curated, reproducible list of all relevant kidney-related genes known to date. This project aims to provide a unified and standardized database of kidney disease-associated genes, contributing to improved diagnosis, treatment selection, and monitoring of kidney diseases. The database is designed to be automatically updated on a regular basis, ensuring the incorporation of the most up-to-date genetic findings in kidney research.
The Kidney-Genetics Atlas contains information for about 3.000 kidney-associated genes. This information was gathered from various reliable sources, such as Genomics England PanelApp, PanelApp Australia, PubTator, OMIM, Orphanet, clinical diagnostic panels, and comprehensive literature review.
The Kidney-Genetics Atlas is publicly available and accessible through GitHub. Furthermore, the database is automatically and regularly updated to ensure its currency and relevance. The documentation also shows the current result from each analysis and the merged list of genes as filterable data tables.
Please explore The Kidney-Genetics Documentation hosted on GitHub pages and build with bookdown.
The repository has the following structure:
.
├── analyses/
│ ├── 01_PanelApp/
│ │ ├── data/
│ │ ├── results/
│ │ └── 01_PanelApp.R
│ ├── 02_Literature/
│ │ ├── data/
│ │ ├── results/
│ │ └── 02_Literature.R
│ ├── 03_DiagnosticPanels/
│ │ ├── data/
│ │ ├── results/
│ │ └── 03_DiagnosticPanels.R
│ ├── 04_HPO/
│ │ ├── data/
│ │ ├── results/
│ │ └── 04_HPO.R
│ ├── 05_PubTator/
│ │ ├── data/
│ │ ├── results/
│ │ └── 05_PubTator.R
│ ├── A_MergeAnalysesSources/
│ │ ├── data/
│ │ ├── results/
│ │ └── A_MergeAnalysesSources.R
│ ├── B_AnnotationHGNC/
│ │ ├── data/
│ │ ├── results/
│ │ └── B_AnnotationHGNC.R
│ └── AnnotateMergedTable.R
└── functions/
├── blueprintgenetics-functions.R
├── hgnc-functions.R
├── hpo-functions.R
├── natera-functions.R
├── NCBI-datasets-v2-API-functions.R
├── phantomjs-functions.R
└── PubTator-functions.R
- The
analyses/directory contains the R scripts for different analyses. - The
functions/directory contains the necessary functions for HGNC processing. - The
data/sub-directory in each analysis folder stores the input data files, including the publication-specific files and the curated overview Excel table. - The
results/sub-directory in each analysis folder stores the generated results.
This project is licensed under the terms of the MIT license. For more information, please refer to the License file.
Bernt Popp
- https://twitter.com/berntpopp
- https://github.com/berntpopp
- https://orcid.org/0000-0002-3679-1081
- https://scholar.google.com/citations?user=Uvhu3t0AAAAJ
Constantin Aaron Wolff
Nina Rank
Jan Halbritter
If you have any questions, suggestions, or feedback, please feel free to contact us.