About Subio PlatformThe free software for the integrated analysis of various omics data.

For RNA-Seq, microarrays, and more

Work on a usual Windows or Mac

No command-line. Best for biologists.

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FREE Download

To download Subio Platform, enter your information below, agree to the terms and conditions, and click the download button.

System Requirements

  • Windows 10 (64-bit) / macOS 10.14 Mojave or later
  • 2 GHz or faster processor
  • 4 GB or more of RAM
  • 5 GB or more of available hard-disk space
  • 1024 x 768 display

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License Agreement and Privacy Policy

Subio Platform End User License Agreement version 1.4

This Agreement, and any new versions, between Subio and You, covers all Your use of Subio Platform and Plug-ins from any terminals. Unless You have another agreement directly with Subio that controls and alters your use or distribution of Subio Platform, the conditions of the applicable license agreements below apply to you.

1. Definitions.

this End User License Agreement, as may be renewed and/or amended from time to time.
You (or Your)
an individual or a legal entity exercising rights under, and complying with all of the terms and conditions of, this License or a future version of this License issued under Section2.8.
Subio Inc., headquartered in Amami island, Japan.
Plug-in Partner
an individual or a legal entity who develops and provides Plug-ins, which are distributed together with Subio Platform.
Subio Platform
Subio Platform, which Subio creates, owns and distributes exclusively. All Plug-ins depend on Subio Platform and they don't work alone nor even start without Subio Platform.
a software created by Subio or Plug-in Partners that works with, adds a variety of functionalities to and distributed together with Subio Platform. You will Activate a Plug-in to use it from a computer installing Subio Platform.
Activate (or Activation)
to authorize one computer to use a Plug-in for one year, by exercising a Serial Number.
Activation Key
a file created as a result of Activation, and it is necessary for Subio Platform to access to the Activated Plug-in.
Serial Number
Plug-in customers will purchase Serial Numbers from Subio or a reseller. Serial Number can be exercised only one time from a computer which is connected to the internet.

2. License and Restrictions

2.1 License of Subio Platform

Subject to the terms and conditions of this Agreement, Subio hereby grants You a limited, personal, non-commercial, non-exclusive, non-sublicensable, free of charge license to download, install and use Subio Platform on Your computer. You may use Subio Platform and Plug-ins anywhere like universities, research institutions, home or at work.

2.2 No Granting of Rights to Third Parties

You will not sell, assign, rent, lease, distribute, export, import, act as an intermediary or provider, or otherwise grant rights to third parties with regard to Subio Platform, Plug-ins or any part thereof.

2.3 No Modifications

You will not undertake, permit or authorize the modification, creation of derivative works, translation, reverse engineering, decompiling, disassembling or hacking of Subio Platform or any part thereof except to the extent permitted by law. Only one exception is that You are allowed reverse engineering of Subio.jar, Subio64.exe and jp.subio.plugins.b.jar.

2.4 Third Parties

Subio Platform incorporates and distributed together with software which are owned and controlled by third parties. Any such third party software falls under the scope of this Agreement. Any and all other third party software that may be distributed together with Subio Platform will be subject to You explicitly accepting a license agreement with that third party. You acknowledge and agree that You will not enter into a contractual relationship with Subio regarding such third party software and You will look solely to the applicable third party and not to Subio to enforce any of Your rights.

2.5 Use of Plug-ins

Subio Platform incorporates and distributed together with Plug-ins which are owned and controlled by Subio or Plug-in Partners. To use Plug-ins, You must purchase Serial Number for each Plug-in from Subio or resellers. If You buy them in Japan, You are also responsible for paying consumption tax. You will explicitly acknowledge the End User License Agreement of the Plug-in by its Activation. Once You have Activated a Plug-in, You may not change the expiration date and the authorized computer. You are not allowed to try, do nor inform any ways of Activation other than the instruction provided by Subio.

2.6 Prohibition of Plug-in Development

You are not allowed to create and distribute Plug-ins, unless You explicitly sign the Subio Plug-in Partner Agreement or an alternative agreement and comply with the terms and conditions thereof.

2.7 Exclusive Ownership

Any and all IP Rights in Subio Platform, contents of Subio website, all materials and documents which are created by Subio are and shall remain the exclusive property of Subio and/or its licensors. Nothing in this Agreement intends to transfer any such IP Rights to You.

2.8 New Versions of Subio Platform and Plug-ins

Subio, in its sole discretion, reserves the right to add additional features or functions, or to provide programming fixes, updates and upgrades, to Subio Platform and Plug-ins. Subio has no obligation to make available to You any subsequent versions of Subio Platform and Plug-ins. You may have to enter into a renewed version of this Agreement, in the event You want to download, install a new version of Subio Platform.

2.9 Suspension

Subio may, in its sole discretion and to the maximum extent permitted within Your jurisdiction, modify or discontinue or suspend Your ability to use any version of Subio Platform and Plug-ins, and/or disable any Subio Platform You may already have accessed or installed without any notice to You, for the repair, improvement, and/or upgrade of the underlying technology or for any other justifiable reason, including but not limited to, circumstances where You, at Subio's discretion, are in breach of this license, creating problems, possible legal liabilities, or engaging in fraudulent, immoral or illegal activities, or for other similar reasons.

3. Disclaimer of Warranties and Limitation of Liability

3.1 No Warranties

Installing Subio Platform enables You to manage, visualize and analyze Omics data. Subio cannot guarantee that You will always be able to get correct calculations and visualizations, nor can Subio guarantee that You can store data entirely and perfectly without inadequate modifications or losing integrity of the data. Subio Platform and Plug-ins are provided “as is” with no warranties whatsoever; Subio does not, either expressed, implied or statutory, make any warranties, claims or representations with respect to Subio Platform and Plug-ins, including, without limitation, warranties or conditions of quality, performance, non-infringement, merchantability, or fitness for use for a particular purpose. Subio further does not represent or warrant that Subio Platform and Plug-ins will always be available, accessible, uninterrupted, timely, secure, accurate, complete and error-free, nor does Subio warrant any quality of analysis with Subio Platform and Plug-ins.

3.2 Your own Risk

Maintenance of Your computer and backup of Your data is entirely responsibility of You. You may be exposed to information security risks by using Subio Platform and Plug-ins with on-line resources. You further acknowledge and agree that the entire risk arising out of the use or inability to use Subio Platform and Plug-ins remains with You, to the maximum extent permitted by law. You understand, therefore, that You use Subio Platform and Plug-ins at Your own risk.

3.3 No Liability

Subio Platform is being provided to You free of charge. You acknowledge and agree that Subio and its licensors and Subio staff will have no liability in connection with or arising from your use of Subio Platform and Plug-ins. Your only right or remedy with respect to any problems or dessatisfaction with Subio Platform and Plug-ins is to immediately uninstall and cease use of such Subio Platform and Plug-ins. Any indirect, incidental, special or consequential damages (including without limitation any loss of or corruption to data, interruption, computer failure or pecuniary loss) arising out of the use or inability to use Subio Platform and Plug-ins; and any loss of income, business or profits (whether direct or indirect) arising out of the use or inability to use Subio Platform and Plug-ins; any loss or damage which may be incurred by You as a result of;

  1. Any errors or incorrect calculations when using Subio Platform and Plug-ins;
  2. Any interruption or inability to use Subio Platform and Plug-ins or their functionalities due to network error or inaccessibility and unavailability of server;
  3. The suspension or termination of this agreement by You or by Subio for any reason; and
  4. The release or the decision not to release new versions of Subio Platform and Plug-ins to you.

The limitations on Subio's liability to You described above shall apply whether or not Subio or the Subio staff has been advised of the possibility of such losses or damages arising.

3.4 Jurisdiction's Limitations

As some jurisdictions do not allow some of the exclusions or limitations as set forth above, some of these exclusions or limitations may not apply to You. In such event the liability will be limited to the maximum extent possible within the applicable legislation.

4. Miscellaneous

4.1 Entire Agreement

The terms and conditions of this Agreement constitute the entire agreement between You and Subio with respect to the subject matter hereof and will supersede and replace all prior understandings and agreements, in whatever form, regarding the subject matter. Nothing in this clause shall exclude or restrict the liability of either You or Subio arising out of fraud or fraudulent misrepresentation.

4.2 Partial Invalidity

If any provision, or any part of a provision, is found by any court or administrative body of competent jurisdiction to be illegal, invalid or unenforceable, and the provision (or part-provision) in question is not of a fundamental nature, the legality, validity or enforceability of the remainder of the terms and conditions of this Agreement (including the remainder of the term which contains the relevant provision) shall not be affected.

4.3 No Waiver

The failure to exercise, or delay in exercising, a right, power or remedy provided by this Agreement or by law shall not constitute a waiver of that right, power or remedy. If Subio waives a breach of any provision of the terms and conditions of this Agreement shall not operate as a waiver of a subsequent breach of that provision, or as a waiver of a breach of any other provision.

4.4 No Assignment

You are not allowed to assign the terms and conditions or any rights hereunder. Subio is allowed at its sole discretion to assign the terms and conditions or any rights hereunder to any third party, without giving prior notice.

4.5 Applicable Law and Competent Court

The terms and conditions of this Agreement shall be governed by and interpreted in accordance with the laws of Japan and shall be subject to the jurisdiction of the courts of the district of Kagoshima.

4.6 Language

The original English version of this Agreement may have been translated into other languages. In the event of inconsistency or discrepancy between the English version and any other language version, the English language version shall prevail.

You expressly acknowledge that you have read this agreement and understand the rights, obligations, terms and conditions set forth herein. By installing Subio Platform, You expressly consent to be bound by its terms and conditions and grant to Subio the rights set forth herein.

Your current operating system may not to be supported. Choose one from the below.

What can you do with Subio Platform?

When you think of the data analysis, you might imagine only about statistical analysis. However, analysts' realness needs more features. Please take a look at the Analysis Guide, and the black frames indicate what you can do with Subio Platform. They are the fundamentals for efficient work like data management (import, export, search, and extraction), multi-dimensional data visualization, normalization of the raw signals, interactive operation of charts, intuitive gene picking and making a list of them, combining gene lists by the Venn Diagram tool, and so on.

Most of the results generated by plug-in tools are stored in Subio Platform. It means you can use them even after the plug-in license expires, or you can smoothly share the data with those who do not have plug-in licenses.

Various types of omics data on one software

Subio Platform accepts any omics data if it's quantitative. For example, transcriptomics, proteomics, metabolomics, DNA methylation, ChIP, and so on. Measurement technologies can be anything like microarrays, high-throughput sequencing, mass spectrometry, RT-PCR, or others.

In RNA-Seq data analysis, it accepts the raw data (FASTQ files) to allow you process read sequences, apply statistical analyses on the gene expression data, and interpret in the biological context, without command-line skills. You don't need a workstation but can work with an ordinary Windows or Mac computer. If you want to detect and analyze SNPs and indels from the FASTQ file of RNA-Seq, you can do it with Variation Plug-in.

Supported File Formats

Data import; Experimental data files

Importing RNA-Seq FASTQ files Detail
Importing RNA-Seq Data (A Table of Counts / TPM / FPKM / RPKM) Detail
Importing Agilent Microarray Data Detail
Importing Affymetrix GeneChip Data Detail
Importing An Excel Data Detail

Data import: Public datasets

Importing and re-analyzing public microarray data sets from GEO. Detail
Importing TCGA RNA-Seq data Detail
A demonstration of analyzing TCGA-LAML miRNA-Seq data. Detail
Importing and analyzing TCGA methylation data Detail

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High-quality viewers to approach the essence of data

The omics data varies in quality. Any algorithms expect good-quality data and, of course, never work well with if it violates their assumptions. Regrettably, there are many awful analysis results because many researchers execute software without checking their data quality. Subio Platform effectively represents the information to analysts to understand the data and make proper decisions on applying methods.

You might think that the free version has significant limitations. However, the truth is that Plug-ins are not necessary for fundamental data analysis. The professional viewers of Subio Platform help your understanding about the data. You can explore deeper and extract more biological insights than using R or Excel.

Learn more on movies.

A quick and in-depth microarray data analysis. Detail

Details of each viewer.

Scatter Plot (Measurement) View Detail
Line Graph View Detail
Tree View Detail
Pathway View Detail
Genome View Detail
Scatter Plot (Samples) View Detail
Venn Diagram Detail

How important is it to view the data correctly?

How to interpret microarray data? Detail
The dynamic range of microarrays Detail
The dynamic range of RNA-Seq Detail

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The proper visual-aid allows the right normalization

The omics data is not uniform, so that determined normalization scenarios work. And this is why there are so many data sets with odd normalizations and weird conclusions. Subio Platform presents the raw data distribution patterns, and how it shows the effect of every step on the data.

We agree that judging if you are doing right normalization might be difficult for you. So we decided not to make software with automatic normalization, but to offer free online support so that you can consult us any time. Please feel free to request.

Learn more on movies.

Finding a proper sequence of normalization and pre-processing. Detail
How to apply the paired T-test? Detail
How to Use Fill Missing Values Block Detail

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The data management system to turn the data to the asset

The exciting nature of omics data is what you can extract now is not the same as what others can do or what you'll be able to do in the future. So, re-analysis is a vital part of omics data. We admit R and Bioconductor have excellence in statistical analysis, though, they aren't good at data management, and you abandon the value as an asset.

On the other hand, Subio Platform allows you to easily import data sets from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Collecting other researcher's data sets in your toolbox is advantageous to make more use of your data.

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Sharing and collaboration accelerate discovering

We know you often receive Excel or PDF files as the analysis result. But they aren't sufficient to tell you the details of the process nor take part. It's hard for you to be involved in the analysis task. So, Subio Platform alternatively offers a comprehensive data sharing system via SSA file format. If you receive an SSA file, you can immediately examine the process and add your unique analysis.

We'd recommend you stop thoroughly assigning the data analysis task to bioinformaticians because they're human beings with a limited perspective, even if they're specialists in statistics or informatics. The omics data analysis requires various aspects from different knowledge, skills, and experiences. Discussion from different points of view is the key to hit innovative ideas.

Learn more on movies.

The deep sharing of omics data by SSA file. Detail

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Low priced Plug-in system

Commercial software usually limits your access to the data after the license expiration. You have to keep paying to maintain access to your data. We also sell plug-ins, though, most tools in the packages store the result data in Subio Platform. It means you can still access the results even after the license expiration.

So do team members whom you share data via SSA files. They don't need plug-in licenses to open the data. It means you don't need to buy licenses for all members, who you want to participate in the analysis task. They can take part only with the free Subio Platform.

  • No more black-box in the data analysis!
  • Let's involve team members in the analysis task.
  • Let innovative ideas emerge from different perspectives.

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Learn more on movies.

Go to Plug-ins page.

Weak points of Subio Platform

Not Famous.

Almost no researchers know Subio Platform, comparing to Excel, R, or GeneSpring. You might worry about using faintly famed software. Subio set the policy from the beginning that we cut all costs other than development and user support to realize the low prices. We don't hire salespersons. We don't appear at trade shows or on media.

But still, some users have kept using us for over ten years. We've got a firm reputation since 2008. You can, of course, submit manuscripts based on the data analysis with Subio Platform. We will support you when some referees give negative comments.

Fewer Statistical Features

We aim Subio Platform to be simple and easy for biologists. It made us limit statistical features to put in. To compliment this point, we designed Subio Platform so that you can work with both Subio Platform and R/Bioconductor. Subio Platform offers the interactive viewer and data management system, and R does a comprehensive collection of statistical methods. Using them together is the most potent combination.

But in reality, "highly sophisticated" statistical methods are not so useful. A large-scale data analysis project of MAQC concluded that using fold-change and non-stringent P-value is better to generate the concordant and reliable DEGs lists than using only P-value. Additionally, we decided to omit legacy features that are no more useful for recent data. For example, z-score normalization used to be necessary due to the terrible quality of spotted dual-channel microarrays. However, it becomes non-sense as microarray technologies mature. Thus we've kept maintaining the balance of functionality and simpleness of Subio Platform.

Learn more on movies.

Working with R/Bioconductor for further statistical analysis. Detail

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If you compare analysis software, you may focus on statistical features. However, they are not everything to make your work easy and efficient.

Items Subio Platform GeneSpring or
other commercial software
R + Bioconductor Excel + PDF
Visual aid with interactive operations
Statistical analysis tools, automation
To allow trials and errors,
or exploratory data mining
Data management
Data sharing, co-working
Cost of using by team
Technical support, training
Publicity, familiarity
Extensibility (functions, data size,
number of participants)

Customers' Opinion

Dr. John Mac Sharry

University College Cork, Lab Researcher

Dr. John Mac Sharry

It is an excellent user interface and the tutorials are brilliant.

Dr. Reidar Albrechtsen

Univ. of Copenhagen, Professor/Manager

Dr. Reidar Albrechtsen

This subio software platform is very easy to handle, even you include several hundred patients. The response is extremely fast compare with other similar softwares. Al...

Dr. Oleg Gusev

RIKEN, professor/manager

Dr. Oleg Gusev

Very flexible and powerful solution. Great technical support. VERY good advisory support!

Read more customers' comments.

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