Data streamer use cases implementation #24
Description
Summary
Expand library's streaming capabilities with some key use cases that build upon existing variant annotation and multi-omics datasets.
Use Cases
1. Multi-omics variant annotation and prioritization
Chain existing annotators (ClinVar, gnomAD, expression, PPI, scores) into configurable pipelines with evidence-based variant ranking.
Key features:
- Pipeline orchestrator for annotation workflows
- Weighted scoring and ranking algorithms
- Support for disease-specific prioritization strategies
2. Automated training set generation
Build streaming jobs that pull latest ClinVar releases and export balanced, stratified training datasets for ML classifiers.
Key features:
- Automated ClinVar version tracking and updates
- Balanced sampling with configurable stratification
- ML-ready export formats (scikit-learn, XGBoost integration)
3. Cross-tissue expression profiling
Expand Expression Atlas integration to support multi-tissue analysis with differential expression and temporal profiling.
Key features:
- Comprehensive tissue panel coverage
- Developmental stage and condition-specific analysis
- Reusable pipeline components for expression summaries
4. Network-aware variant impact assessment
Overlay variants onto protein-protein interaction networks to assess impact on highly connected regions and critical interfaces.
Key features:
- Graph analytics integration (centrality, connectivity)
- Pathway enrichment analysis
- Network topology-based impact scoring
5. Single-cell enrichment analysis
Analyze variant enrichment patterns across single-cell clusters to identify cell-type specific genetic architecture.
Key features:
- Cell-type specific variant impact analysis
- Cross-cluster comparative enrichment
- Developmental trajectory analysis
6. ROC analysis of missense predictors
Systematic benchmarking of missense prediction tools (CADD, REVEL, AlphaMissense) using ClinVar as ground truth.
Key features:
- Multi-predictor comparison with confidence intervals
- Disease-specific performance stratification
- Ensemble method development and performance tracking