University College Cork, Lab Researcher
Dr. John Mac Sharry
It is an excellent user interface and the tutorials are brilliant.
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.
- Subio Platform downloads: > 12,000
- Plug-ins installations: > 3,000
- Citation (Google Scholar)
- Customer List
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
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
- RNA-Seq FASTQ
- Tab-delimited text
- SOFT（Gene Expression Omnibus）
- BED
- GFF
- SAM / BAM
- BAR（Affymetrix）
- WIG / bigWig
Data import; Experimental data files
| Importing RNA-Seq FASTQ files |
Detail
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|---|---|---|
| Importing RNA-Seq Data (A Table of Counts / TPM / FPKM / RPKM) |
Detail
<p><strong>before 1:50 ; </strong> Importing a table of Counts/FPKM/RPKM of RNA-Seq data.</p>
<p><strong>after 1:50 ;</strong> <span style="font-weight: normal;">Importing gene annotation.</span>
</p>
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| Importing Agilent Microarray Data |
Detail
<p><strong>00:00 - 01:40</strong> Importing 1-color (single channel) data files.</p>
<p><span style="background-color: transparent;"><strong>01:40 - 02:45</strong> Importing 2-color (dual channel) data files.</span>
</p>
<p><strong>02:45 - </strong> Importing 2-color data of dye-swap design.</p>
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| Importing Affymetrix GeneChip Data |
Detail
<p><strong>Before 01:45 ;</strong> Converting CEL files to a table of signals with Affymetrix Expression Console Software.</p>
<p><strong>After 01:45 ;</strong> Import the table of signals into Subio Platform.</p>
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| Importing An Excel Data |
Detail
<p>You may often have microarray or RNA-seq data in an Excel worksheet. This movie shows how to import such data into Subio Platform for visualization and statistical analysis. It's generally and widely applicable to import from Excel.</p>
<p>Please take an <a href="/training" title="/training">Online Training</a> for a full instruction of the data analysis.</p>
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Data import: Public datasets
| Importing and re-analyzing public microarray data sets from GEO. |
Detail
<p>Download "SOFT formatted family file" of GSE records. Subio Platform directly accepts it in "Create New Platform" or "Import Samples" wizard windows.</p>
<p>Please take an <a href="/training" title="/training">Online Training</a> for a full instruction of the data analysis.</p>
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| Importing TCGA RNA-Seq data |
Detail
<p>Subio Platform v1.20.5009 supports importing RNA-Seq data of TCGA or TARGET projects from GDC site. It automatically import not only signal values, but also sample annotation. So you can easily start analyzing or exploring the large omics data sets of a variety of cancers.</p>
<p>Please take an <a href="/training" title="/training">Online Training</a> for a full instruction of the data analysis.</p>
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| A demonstration of analyzing TCGA-LAML miRNA-Seq data. |
Detail
<p>You can analyze TCGA miRNA-Seq data with Subio Platform easily. Please take a look at how to import and analyze the miRNA expression data from AML patients.</p>
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| Importing and analyzing TCGA methylation data |
Detail
<p>Subio Platform v1.20.5031 support automatic import of GDC (TCGA projects) methylation array data. You can easily start analyzing the large data sets of various cancers.</p>
<p>Please take an <a href="/training" title="/training">Online Training</a> for a full instruction of the data analysis.</p>
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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
<p>Although many think that they need statistical tools to analyze microarray data sets, any tools are not essential for the omics data analysis. Reversely, It is not fair to say that "you have to use [a tool] for the microarray data analysis." What's important is that you accurately understand what the data is and how to handle it.</p>
<p>You can learn how to analyze the microarray data set through this tutorial. You can examine the quality of the data of individual samples, to remove noise, to extract differentially expressed genes, to see the relationship between the expression behaviors and chromosomal locations with the free Subio Platform. Also you can search the enriched GO terms and pathways with the <a href="http://david.abcc.ncifcrf.gov/" title="http://david.abcc.ncifcrf.gov/" target="_blank">DAVID Functional Annotation</a>, which is a free web tool.</p>
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Details of each viewer.
| Scatter Plot (Measurement) View |
Detail
<p>Scatter Plot (Measurements) View interactively visualizes data of arbitrary two of sample groups. Drag a sample group from the series panel, and drop upon vertical or horizontal axis to set. You can compare how similar or different between signals between the two. Or you can see the relationship between signal intensities and log ratios of one sample group.</p>
<p>Please request a free <a href="/support" title="/support">Online Support</a>, if you don't know how to use it.</p>
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|---|---|---|
| Line Graph View |
Detail
<p>Line Graph View is useful to visualizes changes of signals among Sample Groups. It's interactive and you can select genes just by drag and drop on the chart. The selected genes are emphasized in the Annotations table in the lower panel as well. You can make a Measurement List of the selected genes by clicking on "Save as Measurement List" button, which is next to the camera icon.</p>
<p>Please request a free <a href="/support" title="/support">Online Support</a>, if you don't know how to use it.</p>
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| Tree View |
Detail
<p>Tree View is for browsing a heatmap as a result of hierarchical clustering. A heatmap image on PDF is dead, but this view is interactive. You can traverse nodes, select genes under a node and select samples.</p>
<p>Please request a free <a href="/support" title="/support">Online Support</a>, if you don't know how to use it.</p>
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| Pathway View |
Detail
<p>Pathway View overlays expression pattern as heatmaps or bar graphs on pathway images. You can drag on it to select genes or filter genes by selecting a measurement list. It helps biological interpretation.</p>
<p>Please request a free <a href="/support" title="/support">Online Support</a>, if you don't know how to use it.</p>
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| Genome View |
Detail
<p>Genome View is a genome browser which is essential to analyze data related to genomic locations, like ChIP-Seq, Methyl-Seq, tiling array, CGH array, ChIP-chip, methylation array and so on. Even if you analyze gene expression data, you can use this View to see if the up- or down- regulated genes are located closely or not. If you see dense area of such genes, it may indicates they were controlled by changes of chromosomal structure or epigenetic status.</p>
<p>Please request a free <a href="/support" title="/support">Online Support</a>, if you don't know how to use it.</p>
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| Scatter Plot (Samples) View |
Detail
<p>Scatter Plot (Samples) View is for browsing PCA results, or samples according to your imported profiling. Dots represent sample groups composed of the selected DataSet. Notice that selecting another DataSet changes plots on the chart. You can drag to select sample groups, and Samples involved in the selected Sample Groups are also superimposed in Sample Info tab in the lower panel, and Tree View. These views interact each other.</p>
<p>Please request a free <a href="/support" title="/support">Online Support</a>, if you don't know how to use this.</p>
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| Venn Diagram |
Detail
<p>You can combine measurement lists with Venn Diagram too, to extract genes at intersection, union or difference. Drag&drop a measurement list from Series panel to one of circle of Venn Diagram. If you'd like to combine more than 3 lists, open "# Overlapping" tab. You can input many measurement lists to combine.</p>
<p>Please request a free <a href="/support" title="/support">Online Support</a>, if you don't know how to use this tool.</p>
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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 |
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
<p>Normalization is actually very tricky, because it heavily depends on characteristics of experimental data. That's why we think it can't be automated. Users must make decision to apply suitable normalization and pre-processing to each series. Subio Platform is designed to help your decision making by visual aid, which you can see what happens on data at each step.</p>
<p>Going through trials and errors is the best way to learn about omics data. You can recall pre-set, your saved or currently-applied scenario by one click. So you don't need to be afraid of collapsing data. Try as much as you can, and we're happy to help you via online support. It makes your understanding the data in depth.</p>
<p>Please take an <a href="/training" title="/training">Online Training</a> for a full instruction of the data analysis.</p>
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| How to apply the paired T-test? |
Detail
<p>Clinical data have individual differences and it often makes detecting changes difficult. <br />If you can make pairs of samples from same patients, you can cancel individual difference and focus on effects of the parameter.</p>
<p>Please request a free <a href="/support" title="/support">Online Support</a>, if you don't know how to do this.</p>
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| How to Use Fill Missing Values Block |
Detail
<p>If you need "Fill Missing Value" block, it meas the data needs a bit tricky procedure. RNA-Seq or ChIP-Seq data based on Next-Gen Sequencing technologies or proteomics data from Mass must involves lots of data lacks or '0' signals theoretically. You need to be careful about handling such data, and this demo shows how to make such data more understandable in the biological context with "Fill Missing Values" block.</p>
<p>Please request a free <a href="/support" title="/support">Online Support</a>, if you don't know how to use this tool.</p>
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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.
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
<p>After you analyze omics data with wide variety of biological information, export all data (e.g. gene annotations, sample information, experimental data, result of statistical analysis, PDFs and so on) into one archive (ssa) file. Your collaborators can completely reconstruct what you saw on their PCs just by drag-and-drop the ssa.</p>
<p>This is the easiest way of omics data sharing at the lowest cost.</p>
<p>Please request a free <a href="/support" title="/support">Online Support</a>, if you don't know how to do this.</p>
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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.
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
<p>Subio Platform is a free omics data browser, and you can add analysis tools by activating plug-ins. If you can use R and Bioconductor, you can use Subio Platform with such external tools, too. Even if you can't write code by yourself, maybe you can copy&paste to do it. Although <strong>this demo is in Japanese</strong>, you can get to know how to do it.</p>
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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 |
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| 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
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...
RIKEN, professor/manager
Dr. Oleg Gusev
Very flexible and powerful solution. Great technical support. VERY good advisory support!