Functional Annotation of Variants Online Resource
Beta · Production
Web frontend for FAVOR. Variant annotation, genome browsing, and an agent for functional interpretation.
- FAVOR Agent: Claude Code for variant interpretation. For biobank-scale rare-variant analysis, see FAVOR CLI.
- Structured RAG over the knowledge graph: plain-English queries compile into one server-side plan across Kuzu, ClickHouse, and parquet. N-hop traversals finish in one round-trip instead of N API calls.
- Seven graph modes:
chain: multi-hop (Disease <-> Gene <-> Drug, Variant <-> Gene <-> Pathway)neighbors: direct linkscontext: surrounding factscompare: two entities side by sideaggregate: group and countenrich: statistical overrepresentationpaths: shortest path between two entities
- Multi-step workflows with stateful agents, e.g.:
- variant list → gene → function → pathway, with GWAS stats
- variant → predicted cell effect (multi-omics, IGVF)
- variant → measured cell effect (CRISPRi, MPRA, MAVE, base editing)
- Generative UI: ten inline chat components (bar, comparison, distribution, enrichment, heatmap, network, protein structure, QQ, scatter, stat card).
- Persistent workspace: variant lists, tool outputs, pinned entities across turns.
- AlphaGenome: async submit-and-poll for DeepMind's variant-effect predictor.
- 8.9B-variant genome browser: Gosling.js and HiGlass, no client-side aggregation.
- In-browser SQL: DuckDB WASM over parquet.
- Server-side tables: TanStack Table with backend pagination, sort, filter, column select.
- Interactive knowledge graphs: Cytoscape and XYFlow over variant, gene, disease, drug.
- Locus plots: Manhattan, QQ, tissue heatmaps, allele-frequency distributions.
- Universal search across variants, genes, diseases, drugs, studies. Typeahead, intent routing.
- Variant pages: annotation, GWAS, gnomAD ancestry, tissue QTLs, ChromBPNet, allelic imbalance, methylation.
- Gene pages: variant scan, summary stats, pathways, drug targets.
- Disease and drug pages: Open Targets GraphQL, evidence summaries.
- Regulatory genomics: cCRE, QTL, enhancer-gene links, chromatin states, loops.
- Batch annotation: variant list upload, parquet validation, analytics runs, tissue enrichment packs.
- Auth: cookies, quotas, personal API keys, authenticated SSE proxy.
- Shareable URLs: deep links round-trip for browser, search, and agent state.
- Type-safe API: feature-isolated clients, boundary parsing into branded types.
Prerequisites: Node.js 22+, pnpm
git clone https://github.com/vineetver/favor.git
cd favor
pnpm install
cp .env.example .env.localEdit .env.local:
NEXT_PUBLIC_API_URL=https://api-v2.genohub.org/api/v1
FAVOR_API_KEY=<your-token>To get an API key: go to favor-beta.genohub.org, log in, click your avatar, go to Settings, and generate a token.
pnpm dev # http://localhost:3000Next.js 16 (App Router), React 19, Tailwind CSS v4, shadcn/ui, TanStack Query, AI SDK (OpenAI + DeepSeek), Cytoscape, XYFlow, Gosling.js, DuckDB WASM, Plotly, Recharts.
| Environment | URL | Branch |
|---|---|---|
| Beta | favor-beta.genohub.org | beta |
| Production | favor.genohub.org | master |
Zhou H, Verma V, Li X, et al. FAVOR 2.0: A reengineered functional annotation of variants online resource for interpreting genomic variation. Nucleic Acids Research, 54(D1), D1405-D1414 (2026). DOI: 10.1093/nar/gkaf1217
Zhou H, Arapoglou T, Li X, et al. FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Research, 51(D1), D1300-D1311 (2023). DOI: 10.1093/nar/gkac966
Li Z*, Li X*, Zhou H, et al. A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies. Nature Methods, 19(12), 1599-1611 (2022). DOI: 10.1038/s41592-022-01640-x
Li TC, Zhou H, Verma V, et al. FAVOR-GPT: a generative natural language interface to whole genome variant functional annotations. Bioinformatics Advances, 4(1), vbae143 (2024). DOI: 10.1093/bioadv/vbae143