Omics Playground 4 - The Newest Key Features

Discover the key features available in the new beta version of Omics Playground.

Published on May 20, 2025.

Omics Playground beta testing

Introduction

The beta version of Omics Playground v4 is now available and we can’t wait for you to explore all the powerful new features we’ve been working on!

While this isn’t the final release, we’re opening it up early so you can explore the new functionalities and help us fine-tune things before the official launch.

Now, when you log into your account, you’ll see a new option to enter testing mode (Figure 1). This lets you try out the latest updates while still having access to the current version you know and use (you’ll be prompted to choose an option at each log in).

Figure 1. Welcome screen in Omics Playground showing the option to choose between version 3 (current stable release) and version 4 (beta with new features for testing, coming in the next official update).

The beta testing period will run for approximately one month. After that, all users will be automatically transitioned to the new version.

Curious to see what’s new? Below are a few key highlights! 

1. Multi-Omics Features

Using multiple methods, including MOFA, MixOmics and Deep Learning, you can now test the multi-omics analysis capabilities of Omics Playground with your proteomics, transcriptomics and metabolomics datasets.

Lasagna Muti-Omics Analysis in Omics Playground
Figure 2. LASAGNA model for multi-omics analysis in Omics Playground. Note: The interface shown may slightly change, as this version is actively being updated and refined by our team.

To access the multi-omics features, you’ll need to go through the standard data upload process. However, be sure to select the “multi-omics (beta)” option, then upload or choose the datasets you want to analyze (Figure 3).

Multi-omics data type upload in Omics Playground 4
Figure 3. Multi-omics data type selection in Omics Playground 4 (beta).

When uploading files for multi-omics analysis, you’ll see several options available (Figure 4):

  • Multi-CSV: Upload up to three separate CSV files (one each for transcriptomics, proteomics, and metabolomics data).
  • PGX: Select previously uploaded datasets (.pgx) from your library.
  • Single-CSV: Upload a single CSV file that combines transcriptomics, proteomics, and metabolomics data in one dataset instead of uploading three separate files as in the Multi-CSV option.

Be sure to follow our data preparation guidelines when uploading new datasets.

⚠️ When uploading a single-csv file, you need to add a prefix to each feature name to indicate its data type. This tells the platform whether the feature is a gene, protein, or metabolite. Use the following prefixes:

  • “gx:” for transcriptomics (genes)
    Example: gx:ABC
  • “px:” for proteomics (proteins)
    Example: px:A2M
  • “mx:” for metabolomics (metabolites)
    Example: mx:1072

Adding these prefixes is required so the system can correctly process your data.

Multi-Omics input files selection in Omics Playground data upload.
Figure 4. Multi-omics data upload dialog box in Omics Playground 4. Please ensure your data follows our preparation guidelines before uploading new datasets.

2. Metabolomics Support

You can analyze your metabolomics data directly in the platform. Simply select metabolomics (beta) during the upload process (Figure 5), and the system will guide you through the steps.

The same data preparation guidelines you usually follow for other data types, also apply to metabolomics data.

Metabolomics data upload selection in Omics Playground
Figure 5. Data type selection box in Omics Playground data upload.

3. Improved Data Upload for scRNA-Seq Data

Uploading scRNA-Seq data is now simpler with a dedicated module. Step 4 (QC) has been tailored specifically for scRNA-Seq, featuring custom parameters and methods (Figure 6).

scRNA-Seq QC settings in the data upload in Omics Playground
Figure 6. QC step in the scRNA-Seq data upload process within Omics Playground.

4. Custom Species Support

You can now upload a custom species if the one you’re working with isn’t listed. Simply select <custom organism> and provide a custom feature annotation table along with a custom gene set file.

⚠️ When selecting <custom organism>, a GMT file is required to perform gene set enrichment analysis. If the GMT file is not provided, some features may not function as expected.

Custom organism or specie upload in Omics Playground data upload
Figure 7. Organism selection field in Omics Playground.

5. TimeSeries Analysis (beta)

Time clustering groups features that show similar changes over time using KNN, enabling you to identify different trends in gene expression, also known as gene modules.

Be sure to include a time column in your sample file if you want to perform Time Series analysis.

This feature is available in the Expression module.*

Time Series analysis in Omics Playground
Figure 8. Time Series analysis feature in Omics Playground 4.

*To see this feature in your menu, you will need to enable additional beta features. Simply navigate to the settings in the top right corner of your dashboard and toggle the option for beta features as shown in Figure 9.

Beta features toggle in Omics Playground - BigOmics
Figure 9. How to enable beta features in Omics Playground

6. Improved PCSF

PCSF has been improved to better support multi-omics and metabolomics by adding protein-metabolite interactions.

PCSF analysis in Omics Playground 4
Figure 10. PCSF analysis in Omics Playground 4.

Click below to log in to your account and start exploring the new features:

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