⚠ This is a demo site — any data you upload will be deleted once you leave the session. To keep your data, install OmicsBridge locally and use the full power of the interface — see this GitHub page .
The Multi-Omics Platform Built for the Whole Experiment
Modern research generates transcriptome, epigenome, and single-cell data in parallel —
yet most analysis tools address only one modality at a time.
OmicsBridge integrates several omics modalities and 50+ analytical modules into a single,
code-free platform, covering everything from raw data upload to clinical outcome analysis.
Seamlessly connect your multi-omics findings with cancer patient survival,
mutation landscapes, and immune profiles — all without leaving the interface.
Key Features
🔹
Comprehensive Transcriptome Analysis
– Differential expression, gene correlation, GO/GSEA enrichment, heatmaps,
PCA, swarm plots, and transcription factor inference — all the standard RNA-seq analyses covered in one place.
🔹
Clinical Translatability Built In — Bench to Bedside in One Platform
– Evaluate your omics findings directly in patient cohorts: survival analysis,
mutation landscape (OncoPrint/waterfall), immune cell deconvolution, and COSMIC cancer gene annotation —
all within the same interface. A capability not demonstrated in any of the compared tools.
🔹
Epigenomics & Functional Genomics Included
– ChIP-seq, ATAC-seq, CUT&RUN, and CRISPR screen data are supported natively.
These modalities are absent in all comparable multi-omics platforms.
🔹
Persistent Local Database — No More Repetitive Uploads
– Datasets are stored once and instantly accessible across all modules at any time.
A workflow bottleneck that no other compared tool addresses.
🔹
Cross-Dataset Comparison at Scale
– Rank genes by any numerical score (e.g. log fold change) across multiple experiments simultaneously,
and identify reproducible hits in seconds.
Installing OmicsBridge to your local PC
The source code and installation guide is available at
this GitHub page
Please install and set up OmicsBridge to your local PC to use the full power of our interface.
Database and Data Upload
Registered Datasets
Data upload
1. Upload a file
2. Fill in the dataset information
In case of uploading a count data, please make sure that the columns are set to "(Sample name)_Rep#". See wiki for more information
3. Register the dataset
4. Preview
Count & Comparison Data Overview
Dataset Selection
Dataset detail:
Overview and Analysis
Compare Across Datasets
Dataset Selection
First, please select the data type you want to compare. Then, select the datasets for comparison.
Select the datasets to compare below:
Analysis
Inputs and Settings
A table displaying how often each gene ranks in the top or bottom X% of the selected datasets will appear below.
Overlapped Hits
Bar Plot
Inputs and Settings
A bar or scatter plot comparing the score (selected as Y-axis) of each gene across the selected datasets will be generated in the end.
Input Genes
Select a gene below:
Data Information
Plot
Two Datasets Integration
Side by Side Comparison
Direction
Data1
Please select X/Y axis
Data2
Please select X/Y axis
Overlap Genes
Please set the thresholds for the data to which the selected genes are mapped.
Overlap Genes Table
List of the genes
Integration Plot
Plot
Highlight Genes
Highlight specific genes
Filtering
Filtered Area
Selected Area
List of the genes
Clinical Data Analysis
Data Selection
Dataset detail:
Overview and Analysis
Inputs and Settings
Results (Hazard Ratios)
Plots
Inputs and Settings
Correlation table
Plot
Inputs and Settings
Mutation Frequency Results
Plots
Inputs and Settings
Input Genes Table
Gene Expression Comparison Plot
Inputs and Settings
Note: When there are too many subtypes, it takes longer time to visualise and the figure will be messy.
Test Results
Plot
Inputs and Settings
Note: This takes 1~2 minutes depending on the size of the inputted genes. Please be patient.
Signature Score Results
Plots
Note: When there are too many subtypes, it takes longer time to visualise and the figure will be messy.
Deconvolution
Further Analysis
Inputs and Settings
Plot
Inputs and Settings
Correlation table
Plot
Inputs and Settings
Test Results
Plot
Inputs and Settings
Select one gene below
Select cohorts below
Results and Plots
This takes time depending on how many cohorts you use and the size of each cohort. Note: When using all the TCGA, it takes ~30 sec. Please be patient.
Plot
Table
This takes time depending on how many cohorts you use and the size of each cohort. Note: When using all the TCGA, it takes ~2 min. Please be patient.
Plot
Cancer Gene Census (COSMIC)
Please enter gene names below or select a gene set.
If the genes are associated with cancer predisposition, they will appear in the table. Otherwise, the entire database will be displayed.
Inputs and Settings
Result Table
Registered cohort
Upload
Previews
scRNA Data Overview
Dataset Selection
Dataset detail:
Data Overview & Analysis
Plot
Settings
Inputs and Settings
Select a gene below:
Plot
Please select the groups to use in the violin plot below:
Please select the groups to use in the dot plot below:
Please select the groups to use in the pie chart below:
Here, all the genes in the input gene list will be used to calculate the signature score, not the only gene you selected.
Please note that the AUCell method will determine the active gene set in each cell based on the ranking of the gene expression in that cell. So, if you want to use this method to calculate the signature score for a gene set, it is recommended to input a gene set with more than 10 genes.
This takes 1~3 minutes depending on the size of the input genes and the size of the scRNA dataset. Please be patient.
Select the groups to use in the violin plot below:
Epigenome Visualisation
Profile Plot
Inputs and Settings
Select the samples for the profile plot
List of imported datasets:
Plot settings
Enter the coordinates below:
For example, 'chr1:1000000-2000000'.
Plot
Epigenome Visualisation
Inputs and Settings
Selected datasets:
Plot
1. When using BAM files, a wide range (e.g., >100k–200k bp) can cause a memory error and stop the interface (This issue does not occur when using only BigWig files.)
2. If the sample label is missing, try increasing the height of the figure and re-plotting.
IGV
Inputs and Settings
Selected dataset detail:
Plot
Find Enhancer/Promoter
Inputs and Settings
One pair per line, separated by a comma. At least 3 pairs are required.
Example:
Sample1_RNA_Rep1,Sample1_ATAC_Rep1
Results
Potential Enhancers/Promoters
Motif Scan
Inputs and Settings
Motifs
Plot (logo)
Custom Gene Sets
Custom Gene Sets
Add a Gene Set
Tools
Convert Human and Mouse Genes
Inputs and Settings
The conversion is based on the ortholog mapping from Ensembl database.
Please select the conversion direction, input and output gene ID types, and enter the list of genes (line by line). Then click the 'Convert genes' button to start the conversion.
The conversion table and the list of converted genes will be shown on the right side.
Conversion Table
List of Converted Genes
Convert Gene Symbols and Ensembl Gene IDs
Inputs and Settings
The conversion is based on the annotation from Ensembl database.
Please select the species, input and output gene ID types, and enter the list of genes (line by line). Then click the 'Convert genes' button to start the conversion.
The conversion table and the list of converted genes will be shown on the right side.
Conversion Table
List of Converted Genes
Find Gene Positions/Annotations
Inputs and Settings
Please select the method, enter the gene names or genomic coordinates (line by line), and choose the genome. Then click the 'Search' button to get the results.
Search Results
List of Genes/Coordinates
Peak Annotation
Inputs and Settings
Please enter the peak regions (chr:start-end, line by line), choose the genome, and click the 'Annotate' button to get the results.
Annotation Result
Cross-Tabulation Analysis
Table Contents
Group Names
Values
2x2 Table
Statistical Test
Plot
Venn Diagram
Group Information
Overlap Elements
Plot
Network Plot
Input Data
'from' and 'to' are the node names. 'weight' is the edge weight (numeric).
Input Data Table
Plot
The wiki for OmicsBridge is available at this link .