Frequently Asked Questions
General Information
What is NC-Scorer?
NC-Scorer (Nephro Candidate Scorer) is a web-based application designed to help researchers evaluate genetic variants for their potential involvement in kidney disease. It uses a specialized scoring algorithm that combines multiple lines of evidence to prioritize variants and genes for further investigation.
Who developed NC-Scorer?
NC-Scorer was developed by the Halbritter Lab. The project is actively maintained and open to community contributions.
Is NC-Scorer free to use?
Yes, NC-Scorer is completely free and open-source. You can use it for academic and research purposes without any cost. The source code is available on GitHub under an MIT license.
Using NC-Scorer
How do I input a variant for scoring?
You can enter variants in standard HGVS notation (e.g., NM_033380.3:c.1871G>A) in the search box on the home page. The application supports:
- HGVS notation:
NM_001009944.3:c.11798G>A - Genomic coordinates:
chr16:2138253:G:A - rsID:
rs121913240
What do the scores mean?
NC-Scorer generates three main scores that contribute to the overall assessment:
- Gene Score (0-1): Evaluates how likely a gene is involved in kidney disease
- Variant Score (0-1): Assesses the potential pathogenicity of a specific variant
- Inheritance Score (0-1): Evaluates the inheritance pattern compatibility with the disease model
The final Nephro Candidate Score (NCS) ranges from 0-10:
- 7.0-10.0: High priority (strong evidence for causality)
- 3.0-6.9: Moderate priority (requires additional investigation)
- 0.0-2.9: Low priority (limited evidence)
How are scores displayed visually?
The three key sub-scores are visually highlighted throughout the application:
- Each key score has a subtle background color and left border in the primary theme color
- Score chips have a slight elevation effect for a 3D appearance
- Higher scores are displayed in colors ranging from yellow (low) to green (high)
- Critical scores below certain thresholds may be highlighted in orange or red
- The most important scores are displayed with bold text and special visual treatment
How many variants can I process at once?
Using the batch processing feature, you can analyze up to 200 variants simultaneously. Navigate to the "Batch" section in the main menu to access this feature.
Can I save my results?
Yes, you can download your results in various formats:
- JSON: For programmatic processing
- CSV/TSV: For spreadsheet applications
- VCF: For genomic analysis pipelines
All processing happens in your browser for privacy protection - no data is stored on our servers.
Technical Details
What algorithms are used for scoring?
NC-Scorer uses a combination of machine learning models trained on known kidney disease genes and variants, along with rule-based scoring derived from expert knowledge. The scoring system incorporates:
- Functional studies data
- Expression data
- Conservation scores
- Population databases (gnomAD)
- Clinical annotations (ClinVar)
Which genome builds are supported?
NC-Scorer supports both:
- GRCh37/hg19
- GRCh38/hg38 (default)
The application automatically detects the build from your input or allows you to specify it manually.
What technologies does NC-Scorer use?
NC-Scorer is built with modern web technologies:
- Frontend: Vue.js 3 with Composition API
- UI Framework: Vuetify 3 (Material Design)
- Build Tool: Vite
- State Management: Pinia
- Processing: Browser-based with API calls to specialized bioinformatics services
Is the source code available?
Yes, NC-Scorer is open-source. Visit our GitHub repository to:
- View the source code
- Report issues
- Submit pull requests
- Read contribution guidelines
Troubleshooting
My variant isn't recognized
Ensure your variant is in the correct format:
- Use standard HGVS notation (e.g., NM_033380.3:c.1871G>A)
- For genomic coordinates, specify the correct genome build
- Check that transcript IDs are valid and current
The application seems slow
NC-Scorer performs complex calculations and queries multiple databases:
- First-time queries may take several seconds
- Subsequent analyses are faster due to caching
- Enable caching via the cache toggle button in the navigation bar
Why is my variant search timing out?
This can happen when:
- External APIs are temporarily unavailable
- Network connectivity issues
- Very rare or complex variants requiring extended processing
Try again after a few moments, or check your network connection.
How do I view application logs?
Click the log icon in the footer to open the log viewer. This displays:
- API requests and responses
- Processing events
- Errors and warnings
- Performance metrics
Research & Citations
How should I cite NC-Scorer?
If you use NC-Scorer in your research, please cite:
Citation details to be added after publication
This helps us track the impact of our tool and secure continued funding for development.
Are there related publications?
The methodology behind NC-Scorer is based on several key publications in the field of kidney genetics. Check our GitHub repository for the latest citation information.
Getting Help
Where can I report bugs or request features?
Please use our GitHub issue tracker to:
- Report bugs
- Suggest new features
- Ask technical questions
Before submitting, check if the issue has already been reported.
How can I contribute?
We welcome contributions! See our Contributing Guide or the CONTRIBUTING.md file for:
- Code contribution guidelines
- Development setup instructions
- Pull request process