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Quick Start

This page gets you from opening BRIDGE to generating a successful plot.

Goal:

  • start the app
  • load one dataset
  • confirm the dataset is available
  • generate a first plot

If you want the conceptual background before running anything, read Introduction and Methodology first.

Choose your route

Starting point Go here first
You already have a BRIDGE-compatible SQLite database Continue with this page
You have CSV/TSV files but no database Read Data Requirements, then Database Generation
You were given a showcase database Use that database for the steps below
You want the exact processing/integration logic Read Methodology

Step 1: start BRIDGE

Docker:

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

Local:

Rscript app.R user_database.db

Then open:

http://localhost:3838

Expected result:

  • the BRIDGE interface opens in your browser
  • the Data Selection panel is visible

If the app does not open, return to Installation.

Step 2: load one dataset

In the Data Selection panel:

  1. Select the species.
  2. Select one data table.
  3. Select datapoint columns.
  4. Select the matching annotation table.
  5. Click Load Data.

Expected result:

  • the dataset appears in the loaded-datasets area
  • the individual exploration modules become available
  • no table is deleted from the database when it is removed from the session

If no table or annotation appears, check Loading Data and FAQ.

Step 3: generate your first plot

Recommended first plot:

  1. Open PCA.
  2. Click compute.
  3. Confirm that a PCA plot appears.

Alternative first plot:

  1. Open Raw Heatmap.
  2. Click compute.
  3. Confirm that a heatmap appears.

Why start here:

  • PCA and Raw Heatmap give a global view of the loaded dataset.
  • They are good first checks before interpreting differential results.
  • They can reveal obvious sample grouping, outliers, or data-loading issues.

Step 4: decide what to do next

Goal Next module
Check broad sample structure PCA
Inspect raw expression patterns Raw Heatmap
Find differential signals Volcano Plot or DE Heatmap
Inspect candidate genes/features Gene Expression
Interpret significant features biologically Enrichment Analysis
Compare raw trends across datasets Raw Integration
Compare shared significant IDs across datasets Processed Integration

First-run success checklist

  • App opens at http://localhost:3838.
  • The species selector shows the expected species.
  • A data table appears after species selection.
  • A matching annotation table appears.
  • A dataset appears after clicking Load Data.
  • PCA or Raw Heatmap produces a plot.

If the first run fails

Start with these checks:

  • Docker users: confirm ${YOUR_DATABASE} points to the intended SQLite file.
  • Confirm the data table name starts with the selected species.
  • Confirm the table is registered in table_metadata.
  • Confirm the annotation table is registered in annotation_metadata.
  • Confirm identifier columns are present and non-empty.
  • Confirm datapoint columns follow the replicate suffix pattern, for example X6.hpf_1.

For formatting rules, see Data Requirements.