OmicsBridge

Overview

OmicsBridge is a code-free, multi-omics analysis platform that integrates transcriptome, epigenome, and single-cell data within a single interface. With 50+ analytical modules spanning several omics modalities, it covers everything from standard RNA-seq analysis to epigenome visualisation, cross-dataset comparison, and clinical outcome evaluation — all without writing a single line of code. A persistent local database eliminates repetitive uploads, and custom gene sets defined in one module are instantly reusable across all others.

You can try the demo version of OmicsBridge at https://omicsbridge.dkfz.de. Please note that uploaded data there will be deleted after you close the session. If you want to deploy OmicsBridge in your local environment, please follow the instructions below.

Interface overview

Version

Current version: v1.3.2
Release date: November 2026
See Changelog for the release history.

Installation

Please clone this repository first. In the terminal:

git clone https://github.com/htsmto/OmicsBridge.git
cd OmicsBridge

Next, download the necessary data (00_Clinical_dataset.tar.gz and 00_Expression_data_all.tar.gz) from Zenodo, uncompress and place the folders in the OmicsBridge directory:

tar -xzvf 00_Clinical_dataset.tar.gz
tar -xzvf 00_Expression_data_all.tar.gz

Note: You cound skip downloading 00_Expression_data_all.tar.gz, as it only contains demo data.

the final file structure should be:

.
├── 00_Clinical_dataset
├── 00_Expression_data_all      # auto-created as empty if not downloaded
├── app.R
├── data
├── docs
├── install_packages.R          # automated package installation script
├── launch_with_local_R.command # macOS: install packages (first run) + launch, using local R
├── launch_with_local_R.bat     # Windows: install packages (first run) + launch, using local R
├── launch_with_docker.command  # macOS: launch using Docker (no local R needed)
├── launch_with_docker.bat      # Windows: launch using Docker (no local R needed)
├── libraries                   # per-module library loaders (loaded lazily on first tab access)
├── mkdocs.yml
├── modules                     # modularised server and UI code
│   ├── Clinical/
│   ├── DataOverview/
│   ├── Database/
│   ├── DatasetsCompare/
│   ├── Epigenome/
│   ├── IntegrateTwoDataset/
│   ├── OriginalDataset/
│   ├── Tools/
│   ├── scRNA/
│   ├── wiki_document/
│   └── *_module.R              # per-module orchestrators
├── README.md
├── ui                          # app-level UI components (header, sidebar, body, home)
├── wiki
└── www

Quick Start (Easiest — for local computer usage)

New to the command line?

A screenshot-illustrated, step-by-step guide for non-bioinformaticians is available on the Installation Guide for Non-Bioinformaticians page.

This is the easiest way to get OmicsBridge running, and the recommended path for most users.

This Quick Start is for running OmicsBridge on your own computer, where you'll also open the browser. It is not meant for launching OmicsBridge on a remote server (e.g. over SSH with no desktop to double-click from) — if that's your setup, see Launching the App Manually below, which includes SSH port-forwarding instructions.

First, decide whether you'll use your own R installation or Docker, and install that (R from cran.r-project.org, version 4.4.0 or higher; Docker Desktop from docker.com). Then double-click the one file below that matches your system and that choice:

macOS + local R → launch_with_local_R.command
macOS + Docker → launch_with_docker.command
Windows + local R → launch_with_local_R.bat
Windows + Docker → launch_with_docker.bat

That single file does everything: the first time you run it, it installs the necessary libraries — for local R this means running install_packages.R, and for Docker this means pulling the pre-built image — which takes around 10 minutes either way, depending on your internet connection. It then launches the app. On every later run, it skips straight to launching the app, which takes about 10-20 seconds.

Once it's running, a terminal window will tell you when the app is ready and which URL to open in your browser (http://localhost:4191).

Note (macOS): the first time you double-click a .command file, Gatekeeper may block it as "from an unidentified developer." Right-click (or Control-click) the file → Open → confirm Open. You only need to do this once per file.

Note (Windows): the first time you double-click a .bat file, Windows Defender SmartScreen may show a "Windows protected your PC" warning. Click More info, then Run anyway. You only need to do this once per file.

If you'd rather run things manually from the terminal instead of double-clicking, see the sections below.

Dependencies

Docker Image

We provide a Docker image available from Docker Hub:

docker pull htsmto/omicsbridge:latest

This image already bundles every required package, so no R installation or install_packages.R step is needed on your machine — launch_with_docker.command / launch_with_docker.bat handle the docker pull/docker run for you.

Manual Installation of Required Libraries (for a local R environment)

OmicsBridge requires R version 4.4.0 or higher. While it may work with earlier versions, some packages (such as GSVA) might cause unexpected errors. Please ensure you install BiocManager version 3.20 or higher.

Automated Installation (Recommended)

An installation script is provided. Run the following in your terminal from the project root:

Rscript install_packages.R

This installs all required CRAN, Bioconductor, and GitHub packages automatically and prints a summary of installed versions at the end. (launch_with_local_R.command / launch_with_local_R.bat run this for you automatically on first launch.)

Alternative: Manual Installation

## Bootstrap packages (needed to install everything else)
install.packages(c('BiocManager', 'remotes'))
BiocManager::install() # Make sure to install >3.20

## CRAN dependent packages
install.packages(c('shiny', 'shinyjs', 'shinydashboard', 'shinyWidgets', 'shinycssloaders', 'DT', 'dplyr', 'tidyr', 'reshape2', 'stringr', 'ggplot2', 'ggbeeswarm', 'patchwork', 'ggrepel', 'ggraph', 'eulerr', 'visNetwork', 'igraph', 'circlize', 'cowplot', 'colourpicker', 'ggseqlogo', 'survival', 'survminer', 'Rtsne', 'umap'))

## BiocManager dependent packages
BiocManager::install(c('GSEABase', 'clusterProfiler', 'org.Hs.eg.db', 'org.Mm.eg.db', 'fgsea', 'GSVA', 'decoupleR', 'GenomicRanges', 'GenomicFeatures', 'ChIPseeker', 'AnnotationDbi', 'rtracklayer', 'EnrichedHeatmap', 'Gviz', 'igvShiny', 'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19', 'PWMEnrich', 'PWMEnrich.Hsapiens.background', 'AUCell', 'Seurat'))

## GitHub-only packages
remotes::install_github('ebecht/MCPcounter', ref = 'master', subdir = 'Source')
remotes::install_github('dviraran/xCell')

Launching the App Manually

Prefer the double-click launchers described in Quick Start above — this section is for running things by hand instead.

If you are using a Docker image, open your terminal and

docker run -it --rm \
  -v ${Your_path_to_OmicsBridge_directory}:/app \
  -w /app \
  -p 4191:4191 \
  htsmto/omicsbridge \
  Rscript -e "shiny::runApp('app.R', host='0.0.0.0', port=4191)"

You can customise the port number (4191 in this example) as needed. Once running, open http://localhost:4191 in your browser.

Note: If you are running this on a remote server, make sure to forward the port when connecting via SSH. For example:
ssh -L 4191:localhost:4191 your_username@remote_server_address
After logging in, run the Docker command as above on the remote server. Then, open http://localhost:4191 in your local browser to access the app.

If you're using your local R environment instead of Docker, open your terminal and:

cd ${Your_path_to_OmicsBridge_directory}
Rscript -e "shiny::runApp('app.R')"

Note: If you get an error of utils::browseURL (ex. 'browser' must be a non-empty character string), please try:
Rscript -e "shiny::runApp('app.R', launch.browser = FALSE)"

A new browser tab should open automatically. If it doesn't, check your terminal for a message like Listening on http://X.X.X.X:YYYY and navigate to that URL in your browser.

Usage Guide

We provide a comprehensive Wiki for the interface at https://htsmto.github.io/OmicsBridge/. The Wiki contains concise instructions and short demo videos for each visualization and analysis feature.

Citation

A permanent DOI and citation will be provided upon publication.

Contact

For questions, feature requests, or bug reports, please contact:

Hitoshi Matsuo
German Cancer Research Center (DKFZ) Heidelberg
Division Immune Regulation in Cancer
Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
Email: hitoshi.matsuo[at]dkfz-heidelberg.de