OmicsBridge

Overview

OmicsBridge is an intuitive platform that integrates and visualizes diverse omics datasets. Our tool helps researchers identify key genes with functional and clinical relevance, supporting hypothesis generation. It also serves as a centralized database for efficient data storage and access, reducing scattered datasets and improving overall data accessibility.

You can use OmicsBridge through a standalone web interface at https://omicsbridge.dkfz.de. Please note that uploaded data will be deleted after you close the tab. If you want to deploy OmicsBridge in your local environment, please follow the instructions below.

Installation

Please clone this Github repository by running the following commands in your terminal:

git clone https://github.com/Immune-Regulation-in-Cancer/OmicsBridge.git
cd OmicsBridge

Alternatively, you can download the ZIP file from the repository and extract it manually. Note: You may be prompted to install git-lfs when cloning the repository. For installation instructions, please refer to the official Git LFS website.

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

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

the final file structure should be:

.
├── 00_Clinical_dataset
├── 00_Expression_data_all
├── app.R
├── data
├── docs
├── mkdocs.yml
├── README.md
├── wiki
└── www

Alternatively, copy the links above and paste them in a browser to download the files, then uncompress and place them inside the OmicsBridge folder.

Dependencies

Docker Image

We provide a Docker image available from Docker Hub:

docker pull htsmto/omicsbridge:latest

Manual Installation of Required Libraries

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 install the following libraries and ensure you install BiocManager version 3.20 or higher.

## CRAN dependent packages
install.packages(c('shiny','shinydashboard','eulerr','ggplot2', 'ggbeeswarm','patchwork','igraph','tidyr','dplyr','DT','ggrepel','tibble','forcats', 'colourpicker', 'devtools','stringr', 'Cairo', 'Seurat', 'reshape2', 'cowplot', 'survival', 'survminer',"BiocManager", 'visNetwork', 'ggraph', "shinyWidgets", "shinycssloaders", 'ggseqlogo', 'circlize'. 'ggupset'))

## BiocManager dependent packages
BiocManager::install() # Make sure to install >3.20
BiocManager::install(c("GSEABase",'GSVA','fgsea',"clusterProfiler","org.Hs.eg.db","org.Mm.eg.db","decoupleR","igvShiny","GenomicAlignments", "AUCell", 'Gviz', 'PWMEnrich', 'seqLogo', 'PWMEnrich.Hsapiens.background', 'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19', 'EnrichedHeatmap', 'rtracklayer', 'ChIPseeker'))

## Other packages
devtools::install_github("ebecht/MCPcounter",ref="master", subdir="Source")
devtools::install_github('dviraran/xCell')

Launching the App

If you are using a Docker image, open your termiank 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 teminal 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.

Version

Current version: v1.0
Release date: August 2025

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