Installation

BRIDGE can be run with Docker or locally.

For the shortest path to a first plot, use this page together with Quick Start.

Before starting, you need a BRIDGE-compatible SQLite database. If you only have CSV/TSV files, check Data Requirements before creating the database with Database Generation.

Fastest start (Docker)

Run:

docker run -d --rm \
  --name bridge \
  -p 3838:3838 \
  --mount type=bind,src=${YOUR_DATABASE},dst=/srv/data/database.db \
  ghcr.io/paulilab/bridge:latest

Then open:

http://localhost:3838

Local setup

Prerequisites:

• R
• Python
• A BRIDGE-compatible SQLite database

Clone the repository:

git clone https://github.com/paulilab/BRIDGE
cd BRIDGE

Restore the R environment:

renv::restore()

Run the app:

Rscript app.R user_database.db

If you do not have a database yet, go to Database Generation.

First-run success checklist

1. App opens at http://localhost:3838.
2. Species selector shows the expected species.
3. A data table appears after species selection.
4. A matching annotation table appears.
5. Dataset appears after clicking Load Data.
6. PCA or Raw Heatmap produces a plot.

After this works, load a second dataset and test Raw Integration if your goal is cross-omics comparison.