gitools-web

A modern, browser-based genomics matrix explorer. Brings Gitools' full statistical suite to the browser, with a task-driven UX that guides users through load → annotate → explore → compare.

Runs entirely in the browser as a static web app — no server required.

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Features

• Load matrices up to ~300 columns × 20,000 rows (GCT v1.2/v1.3, TSV, Parquet, Arrow IPC)
• Multi-series (multidimensional) cells: multiple named values per gene/sample cell
• Fast WebGL heatmap with pan and zoom at 60 fps
• Row and column annotation tracks from TSV or CLS files
• Group comparison statistics with volcano plot and ranked results
• Search, filter, and sort by annotation fields or by sum across selected columns/rows

Statistical tests

Test	Source
T-test (Welch's, two-sided)	Ported from Morpheus.js (BSD-3)
Signal-to-noise ratio	Ported from Morpheus.js (BSD-3)
Fold change (log₂)	Ported from Morpheus.js (BSD-3)
Mean difference	Ported from Morpheus.js (BSD-3)
Fisher exact	Ported from Morpheus.js (BSD-3)
Mann-Whitney U (Wilcoxon rank-sum)	Original implementation
Z-score / Stouffer's method	Original implementation
Binomial test	Original implementation

P-value corrections: Benjamini-Hochberg FDR (ported from Morpheus.js, BSD-3) and Bonferroni.

Getting started

Run in the browser (development)

npm install
npm run dev

Open http://localhost:5173 and drag a matrix file onto the drop zone.

Build for deployment

npm run build   # output goes to dist/

Deploy the dist/ folder to GitHub Pages, Netlify, or any static host.

Desktop app (Tauri)

npm run tauri build

Produces a native installer in src-tauri/target/release/bundle/:

• macOS: .dmg
• Windows: .msi / .exe
• Linux: .AppImage

Tech stack

Layer	Choice
Language	TypeScript + React + Vite
In-browser query	DuckDB-WASM
Heatmap render	WebGL (custom GLSL shader)
Annotation tracks	Canvas 2D
Statistics	Custom implementations + ports from Morpheus.js
Background compute	Web Workers
UI	Tailwind CSS + shadcn/ui
Desktop shell	Tauri v2

Attribution

Portions of this code are derived from Morpheus.js (Connectivity Map and LINCS at the Broad Institute), used under the BSD 3-Clause License. See LICENSE.morpheus for the full license text.

License

MIT