Omics Playground V3:
A Fresh Look and Exciting New Features
Published on December 14th, 2023
⏱ 9 min read
Introduction
We’re excited to announce the release of Version 3 of Omics Playground. As our team has been hard at work behind the scenes, we are happy to bring you a fresh look and a new set of features that will elevate your omics data analysis experience.
Here is what you’ll find in this latest version:
- An improved interface.
- New Features:
Continue reading to learn more about each of them.
An improved interface
Omics Playground V3 has a refreshed interface with a modernized look. In contrast to V2, changes include a new welcome page and adjustments to menu placement.
When logging in, you will find a welcome page that allows you to choose between uploading new data or using saved datasets (Figure 1). If you wish to explore Omics Playground without existing data, simply click “load example dataset” to begin exploration.
A notable change in the user interface is the repositioning of the main menu and settings tab, now framing your dashboard. The collapsible menu is positioned on the left side of the screen, offering the flexibility to close it for additional plot space. For each analysis tab, you’ll find settings conveniently located on the right side of the dashboard, facilitating the adjustment of parameters and the selection of genes of interest (Figure 1).
Figure 1. The new interface of Omics Playground.
This design allows for a personalized data exploration experience, giving you the flexibility to either monitor settings or maximize workspace for data visualization.
Pro tip: Explore advanced options within each setting tab for a more refined analysis. All necessary tools are easily accessible, and in moments of uncertainty, our team is available through the chatbot in the bottom right corner for expert guidance.
New Omics Playground Features
1. New pathways: WikiPathways and Reactome
We included WikiPathways and Reactome to provide a wider range of biological pathways. You can find both under GeneSets Tab > Pathway analysis (see Figure 2).
Figure 2. WikiPathways in Omics Playground.
2. New visualization: Gene and Geneset UMAPs
A new type of visualization clusters genes or gene sets as a UMAP (Figure 3). This is a very intuitive and visual approach to compare between multiple conditions and to provide insight into co-regulation and shared biological functions.
You can find this new feature under Clustering>Features.
3. Prize-Collecting Steiner Forest (beta feature)
The PCSF constructs a gene interaction network from your data (Figure 4). It focuses on identifying key genes that act as “hubs” in the network, connecting various biological pathways. You can find it under Clustering > PCSF (beta).
Figure 4. PCSF analysis with Omics Playground.
Note: to see this feature in your menu you first need to enable the beta features in the settings at the top right corner of your dashboard (Figure 5).
4. Compare datasets.
Compare different experiments by correlating their fold-change signatures and compare their gene UMAPs (Figure 6). You can even compare transcriptomics and proteomics data in this way. You can find this new feature under Compare>Compare datasets.
5. Data sharing
You now can easily share datasets with your colleagues or collaborators. Here are the steps you need to follow:
- Go to the Load Datasets tab and identify the datasets you want to share.
- Click the 3 dots on the left and Click “Share with user” from the pop-up menu (Figure 7).
3. Provide the email of the person you want to share the dataset with and confirm.
4. You’ll see a prompt when the dataset has been shared (Figure 8). Your colleague will be notified about the dataset shared via email and will be able to accept it in their Omics Playground account.
6. Add custom genesets for analysis
You can now upload a list of custom gene sets for your enrichment analysis. To do so:
- Go to the Load Tab and click on New dataset.
- Select your organism, upload your input files, select your comparisons and go to Compute.
- In the Compute section, click on Computation option and select your GMT file (Figure 9).
Figure 9. Where to upload GMT files in Omics Playground
4. Click 
5. Explore your custom gene sets in the Geneset enrichment analysis tab (Figure 10).
7. Signature explorer
Your Load dataset panel now shows a visual summary of all your signatures in your library in a single UMAP (Figure 11). You can perform a meta-analysis between them in the ‘Compare’ module.
