Subio Platform is data analysis software for RNA-Seq, microarray, DNA methylation, and multi-omics data. It helps you visualize gene expression data, methylation data, and other omics datasets without programming, so you can explore, compare, and interpret your data visually.
Subio Platform helps researchers focus less on tool operation and more on looking at data, making judgments, and understanding the analysis process.
The core features of Subio Platform are free to use.
Start by visualizing and exploring omics data on your own computer.
Windows and Mac compatible.
In RNA-Seq analysis and other omics data analysis, following a tutorial or workflow can produce results.
But during the analysis, you may wonder:
Subio Platform is omics data analysis software that helps you examine data distributions, sample relationships, clusters, and gene expression patterns instead of accepting results as a black box.
By looking at the data before accepting the results, you can move from “I have results, but I am not sure if I can trust them” to a state where you can check the results and make informed decisions.
Try it with your own data.
Windows and Mac compatible.
If you are new to Subio Platform, you can start with a tutorial using demo data.
Start RNA-Seq Tutorial
Trusted by researchers since 2009.
See publicationsand user voices.
With Subio Platform, analysis starts by checking the quality of the data.
As software designed specifically for omics data, Subio Platform helps you visually examine batch effects, outliers, and biases in the data distribution.
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Subio Platform does not compete with R or Python. It complements them.
Subio Platform handles intuitive visualization and data management, while R and Python handle advanced and specialized statistical computation. This lets you extend your analysis when needed without losing visual understanding of the data.
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A new style of RNA-Seq data analysis | Analyze with R / Python × Visualize and manage data with Subio
| Approach | Ease of Use | Interpretability | Flexibility |
|---|---|---|---|
| Command-line tools (R, Python) | Moderate | Moderate | High |
| GUI tools (especially browser-based) | High | Moderate | Limited |
| Subio Platform (GUI + script integration) | High | High | High |
Even if you cannot write code yourself, generative AI can help you create R / Python scripts. However, it is still the analyst who must judge whether the results are appropriate for the research purpose and whether the analysis is valid.
In this new environment, the ability to read generated code and evaluate whether the results fit the research question will become more important than the ability to write code from scratch.
Practical workflows are explained in the following articles:
When you analyze data with Subio Platform, you can import not only your own experimental data, but also public datasets from sources such as GEO and TCGA. Over time, your analysis results can become a searchable, reusable, living archive.
Past data does not have to remain just a record.
It can become a research asset, waiting to be rediscovered from a new perspective.
Case Study 339: Gene expression is consistent across datasets. miRNA is not.
When multiple hepatocellular carcinoma (HCC) datasets were compared, gene expression remained consistent across platforms (RNA-Seq and microarrays), whereas miRNA expression showed striking discrepancies between datasets.
Importantly, miRNA expression appears internally consistent within each dataset.
However, this issue cannot be recognized from a single dataset—it only becomes evident when multiple datasets are compared.
Case Study 189: Cross-study consistency builds confidence
When independent datasets on mouse mammary gland development were compared, highly consistent expression patterns were observed across studies.
This demonstrates that by accumulating data and enabling cross-dataset comparisons, it becomes possible to assess the reliability of information and identify results that can be trusted.
Scan Genes over Series tool (System Plug-in):
This feature enables searches similar to GEO Profiles, but applied to your own accumulated datasets within Subio Platform.
You can instantly explore how a gene of interest behaves across different datasets (Series), transcending differences in species and experimental platforms.
Subio Platform can import a wide range of omics data, including RNA-Seq, microarray, DNA methylation, proteomics, ChIP-Seq, and ATAC-Seq data. It not only helps you visualize and analyze these datasets, but also allows you to store them in a reusable form. You can also import public datasets from databases such as GEO and TCGA for re-analysis and comparative analysis.
If you find certain datasets difficult to handle, you can use Subio’s Data Analysis Service.
We can process your requested datasets and deliver them in SSA format, ready to be added to your archive.
Subio Platform’s original SSA file format is not just a way to save analysis results. It is a way to make RNA-Seq and other omics analysis results reusable.
An SSA file can package raw data, statistical analysis results, parameters, research notes, and related documents such as PDFs into a single file.
Recipients do not need an additional license. With a simple installation, they can immediately reproduce, explore, and reanalyze the data.
The core features of Subio Platform are free to use. Start by visualizing and managing data, or by reanalyzing public datasets, on your own computer.
If you want to run commonly used analyses more quickly or use advanced analysis functions, plug-ins can help.
Learn more:
What You Can Do with the Free Core Features of Subio Platform
Subio Platform provides tutorials, troubleshooting resources, case studies, and software guides for researchers who want to learn and analyze data independently. You can start by exploring the data yourself and building a deeper understanding of its structure.
If you feel unsure about following procedures on your own, or if you want to save time in your analysis, you can also use Subio’s data analysis service or one-on-one online training. Choose the support that best fits your research stage.
The core features of Subio Platform are free to use.
Please fill in the form below and download the Windows or Mac version.
To download Subio Platform, enter your information below, agree to the terms and conditions, and click the download button.
With Subio Platform, visualization and data management are available for free.
Statistical analysis, clustering, differential expression analysis, and other analyses can also be performed by combining Subio Platform with R or Python. However, writing and adjusting code can take time.
Plug-ins let you run commonly used analyses more quickly, so you can spend less time on operations and focus more on understanding the data and interpreting the results.
Some advanced functions are available as plug-ins.
If you want to learn the workflow using GEO data, we recommend starting with the RNA-Seq analysis tutorial.
Start RNA-Seq Tutorial
If you want to analyze your own data or public datasets of interest more efficiently, you can also use Subio’s data analysis service or online training.
View Data Analysis Service
View Online Training