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

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.

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.

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.

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

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

A Quarto gallery of Shiny apps and packages for computational biology