Unlock the Full Potential of Your Omics Data
Acquiring and analysing multiple omics datasets is now common practice, even in labs without a strong bioinformatics background.
However, integrating and managing large, multidimensional datasets remains a challenge, often leading to underutilised data and missed discoveries.
Why Use Our Interface?
🔹 Seamless Data Integration – Combine datasets from multiple omics layers to uncover hidden biological insights.
🔹 Custom Gene Sets – Define key genes from clinical or functional data and apply them across experiments.
🔹 Comparative Analysis – Identify trends and reproducibility by comparing numerical scores across datasets.
🔹 Clinical Relevance Exploration – Evaluate genes in patient cohorts to assess therapeutic significance.
🔹 Interactive Visualisations & Quick Analysis – Adjust thresholds, filter data, and perform GO analysis or GSEA—no coding required.
🔹 Our platform also functions as a centralised database, ensuring stress-free access to your datasets at any time.
Installing OmicsDBridge to your local PC
The source code and installation guide is available at this github page.
Please note that the data you upload to this website will be deleted once you leave the session. Please install and set up OmicsBridge to your local PC to use the full power of our interface.
Make your data work for you. Start uncovering meaningful biological connections today.
Database and Data Upload
List of the datasets
Data upload
1. Upload a file
2. Fill in the dataset information
In case of uoloading a count data, please make sure that the columns are set to "SampleName_Rep#". See wiki for more information
3. Click the button below
Preview:
Data Overview
Dataset Selection
Dataset detail:
Overview and Analysis
Data table
Inputs
Choose gene(s) from the table blow:
Expression scores
Swarm Plot
List of the available group names
List of sample names ▼ (click here)
Inputs and Settings
Choose a row from below:
Plot
List of the sample names
Inputs and Settings
Choose the samples to use below:
Plot
Expression scores
List of the genes in each cluster.
Plot
Settings
List of sample names ▼ (click here)
Data table
Main plot
Display Options
Choose X and Y axis:
Highlight the genes of interest
Highlight filterd genes or gene sets in the plot
Futher filtering
Apply filtering
Information of genes of interest
Outliers Information
List of the genes
Pathway Genes Information
List of the genes
Custom Gene Sets Information
List of the genes
Selected Area Information
Downstream analysis
Settings
This takes 1~3 minutes depending on the size of the input. Please be patient.
Results & Plots
(DecoupleR analysis. Available only for RNAseq DEG data processed from DESeq2)
Settings
Plots & Resutls
Custom Genesets Information
Custom Gene Sets
Add a Gene Set
Compare across datasets
Dataset selection
Dataset setection
Anlaysis
Filtering criteria
A table displaying how often each gene ranks in the top or bottom X% of the selected datasets will appear below.
Overlapped hits
barplot
Analysis options
Gene select table
Select a gene below:
Data information
Plot
Integrate two datasets
Side by Side comparison
Direction
Data1
Please select x/y axis:
Data2
Please select x/y axis:
Overlap genes
Please set the threshoolds for the data to which the selected genes are mapped.
Overlap genes table
List of the genes
Integration Plot
Plot
Display options
Filtering
Filtered area
Selected area
List of the genes
Clinical data
Data selection
Dataset detail:
Overview and Analysis
Inputs and Settings
Results (Hazard Ratios)
Plots
Inputs and Settings
This calculates the correlation with all the genes. It takes 2~4 minutes. Please be patient.
Correlation table
Scatter plot
Inputs and Settings
Results (Mutation Frequency table)
Plots
Input and Setting
Input genes table
Plot for Gene expression comaprison
Input 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.
Results (Signature scores)
Plots
Note: When there are too many subtypes, it takes longer time to visualise and the figure will be messy.
Deconvolution
Futher analysis
Input and Setting
Results and Plots
Plot
Graph options
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
Cacner Gene Census (COSMIC)
Genes input
Registered cohort
Upload
Quick upload guide ▼
- Make sure that the column name for samples (or patients IDs) is set 'sample' and for genes is set 'id'.
- The fist column of the gene expression file must be the samples
- The Cohort name is mandatory and must be unique.
- Avoid special characters; use only alphabets, numbers, underscores and dots.
Previews
scRNA
Dataset selection
Dataset detail:
Data Overview & Analysis
Plot
Setting
Inputs and Settings
Select a gene below:
Plot
Inputs and Settings
This takes 1~3 minutes depending on the size of the input genes and the size of the scRNA dataset. Please be patient.
Plots
Select the groups to use in the violin plot below:
Inputs and Settings
Plot
Inputs and Settings
Select a gene below:
Plot
Select the groups to use in the violin plot below:
Inputs and Settings
Select a gene below:
Plot
Genome Browser (IGV)
IGV
Inputs and Settings
List of imported dataset:
Profile Plot
Inputs and Settings
Selected dataset detail:
Plot
Tools
Convert Huamns genes with Mouse genes
Inputs and Settings
Conversion Table
List of converted genes
Convert Ensemble gene ids with Gene symbols
Inputs and Settings
Conversion Table
List of converted genes
Find the genomic loci
Inputs and Settings
Search results
List of genes/coordinates
Cross-tabulation analysis
Table contents
Group Names
Values
2x2 Table
Statistic test
Plot
Venn Diagram
Information of each group
Show the overlapping elements
Plot
Network plot
Input
The input data table
Plot
The wiki for OmicsBridge is available at this link .