A free, browser-based tool for mapping marine and non-model organism omics results onto biological pathways. It ingests differential expression (DEG), differential methylation (DMR), proteomics, metabolomics, or multi-omics tables; maps identifiers to pathway entities directly or through orthology to a reference organism; and produces interactive, publication-ready pathway diagrams using open pathway resources (WikiPathways and Reactome).
Everything runs client-side. Your data never leaves your computer, and no API key is required for ordinary use.
- Flexible input — CSV / TSV / XLSX / pasted text; multiple tables; automatic column detection with full manual override.
- Built for non-model organisms — direct, ortholog-reference, or user-supplied ortholog-table mapping, with one-to-many and distant-reference ambiguity made explicit.
- Transparent by design — a clear distinction between a descriptive mapping summary and a statistical enrichment analysis (Fisher's exact + Benjamini- Hochberg, only when a background universe is supplied), plus visible uncertainty warnings throughout.
- Interactive visualization — zoom/pan pathway diagrams, multi-omics node styling, colorblind-aware palettes, per-node detail panels, and SVG/PNG export.
- Reproducible — deterministic layout and scoring; exportable audit tables, session files, and an auto-generated methods paragraph.
- Open pathway data only — WikiPathways (CC0) and Reactome (CC-BY 4.0). KEGG is link-out only; no proprietary images are redistributed.
# Node 20+ recommended
npm install
npm run dev # start the dev server
npm run build # production build to dist/
npm run preview # preview the production build
npm test # run the unit + integration test suite
npm run typecheck # TypeScript type checkingThen open the app and click Load demo data to explore a bundled multi-omics example end to end.
The app is a static site — deploy dist/ to any static host.
- GitHub Pages: build with a base path matching your repo, e.g.
then publish
VITE_BASE=/marine-pathway-mapper/ npm run build
dist/. The base path defaults to/for local dev and other hosts. - Netlify / Vercel: build command
npm run build, publish directorydist.
React + TypeScript + Vite + Tailwind CSS, D3.js for visualization and layout, papaparse and SheetJS (xlsx) for client-side parsing, Vitest for testing.
- User Guide — full walkthrough of the six-step workflow.
- Data Model — types, the transformation pipeline, and the transparency guarantees.
- Sources & Attribution — bundled pathways, licenses, and how they were obtained.
The sample_data/ directory (also served at public/samples/) contains example
DEG, DMR, metabolomics, and ortholog tables you can load from the Upload page.
The suite covers column detection, identifier normalization, one-to-many ortholog handling, mapping summaries, the color scale, CSV/TSV export, enrichment statistics, and an end-to-end pipeline run on the demo dataset.
npm testThe bundled pathway library is a curated static core for offline use, not the complete WikiPathways/Reactome collection (live API synchronization is a planned modular extension). Pathway layouts are readable approximations, not byte-for-byte reproductions of the source diagrams. Ortholog-based mappings are annotations, not direct evidence — interpret results with orthology quality, annotation completeness, and background choice in mind. Pathway overlap does not imply causation.
Application code: MIT. Bundled pathway data retains its original source licenses (WikiPathways CC0, Reactome CC-BY 4.0). See docs/SOURCES.md.