variant-interpretation

Personal Cancer Genome Reporter (PCGR)

genetic variant expressions, annotation, and filtering for great good.

Variant Interpretation Pipeline

API-first variant triage pipeline combining genomic filtering, annotation, and LLM-driven interpretation for clinical genomics workflows

PhenoSV: Interpretable phenotype-aware model for the prioritization of genes affected by structural variants.

MetaDome is aimed at professionals in the (bio-)medical field of human genetics who wish to visualize the position of their variant of interest in the context of general population-based genetic variation, and provides detailed information on pathogenic variants found across homologous protein domain positions, for GRCh37 and GRCh38.

GUANinE Benchmark Dataset and Tools

hReg-CNCC is a high-quality Regulatory network of Cranial Neural Crest Cell (CNCC), built by consensus optimization.

SpecVar is a convenient tool for estimating interpretable genetic correlation of human complex traits and annotating the SNPs with context specific regulatory networks

LOVD+ -- LOVD for diagnostics: analysis of whole-exome data using LOVD.

ACMG Assistant is a student-level, research-oriented variant classification tool developed to explore the practical application of ACMG/AMP 2015 and 2023 guidelines. It combines automated retrieval of annotation data from public APIs with structured interactive evidence collection to support systematic variant interpretation.

MCP gateway federating 21 biomedical MCP servers — gnomAD, ClinVar, HPO, UniProt, Ensembl VEP, PanelApp and more — behind one Streamable-HTTP endpoint, with collision-free namespaced tools and BM25 tool search.

Local-first DNA and VCF analysis copilot for evidence-bound genomics workflows, confidence tiers, and Claude/Codex support.

Multi-source germline variant annotation pipeline

Genetik varyantların patojenite analizini; XGBoost, GNN ve Transformer tabanlı hibrit bir "Stacking Ensemble" mimarisi ile gerçekleştiren; biyoinformatik temelli, açıklanabilir (XAI) klinik karar destek sistemi.

Segregation analysis for clinical variant interpretation

Ablation of rule-based models for therapeutic exon-skipping targets in Duchenne muscular dystrophy (DMD) — reading-frame arithmetic, splice topology and domain constraints, tested layer by layer against public genomics data.

Clinical genomic analysis with 105 curated agent skills. Research overview, results and invitation-based web access. System code is not publicly released.

Turn a candidate gene list and a disease context into a ranked, evidence supported review. Deterministic keyless core, optional Claude agent layer.

A Quarto gallery of Shiny apps and packages for computational biology