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Share and Visualize Seurat and Scanpy Objects Using C-DIAM


The Collaboration Problem

Seurat (for R users) and Scanpy (for Python folks) have long been favorites for analyzing single-cell RNA-seq data. With their robust capabilities, you can perform everything from clustering cells to running UMAPs, identifying markers, and predicting cell types—essentially, you can do it all.


But when it comes time to share the results with the broader team, things can get complicated. As useful as these tools are for analysis, the process of sharing those results, especially between bioinformaticians, biologists, and other stakeholders, can feel like a mini project in itself.


More often than not, results are exported as static plots and tables, dropped into PowerPoint slides, and passed around for review. This leads to a cycle of back-and-forth: biologists raise questions, bioinformaticians re-run analyses, and the loop starts over.


Let’s be honest: it’s not ideal.


Making Single-cell Data and Results More Accessible and Shareable

To simplify collaboration, we’ve developed a feature in our C-DIAM Multi-omics Studio—our web-based platform for omics data analysis—that enables seamless sharing and interactive visualization of Seurat and Scanpy objects.


Now, you can easily upload and share Seurat or Scanpy objects—without any installations, coding, or technical knowledge required. Simply drag and drop your objects into the platform, and get them transformed into beautiful, clickable, zoomable, and shareable dashboards.


This makes the process of exploring, reviewing, and collaborating on single-cell data much more accessible for everyone on the team, from computational scientists to bench scientists.


No installations. No coding. Just the data, ready to explore—by anyone on the team.


What You Can Do:


Step 1: Upload .rds or .h5ad files in just a few clicks

Zip up all your coordinates, clustering results, cell type annotations, metadata—everything you’ve worked on in Seurat or Scanpy—and drop it right into the C-DIAM platform. The upload process is quick and intuitive.



Step 2: Share your work with a link

Once the data is uploaded, you can generate a shareable link. Send it off to your collaborators or PI, and they can explore the data and results directly in their browser, no installations needed.



Step 3: Let collaborators explore the dataset

Collaborators who have access to the dataset can dig into the data themselves. Visualize the UMAP that has been generated in Seurat/Scanpy, together with the clusters and metadata fields, while testing out markers, and even running additional analytics—on the fly.




Supported Analytics

C-DIAM Multi-omics Studio isn’t just about making data shareable. It’s also about providing a rich, interactive experience for users to analyze and explore the data together. With a user-friendly point-and-click interface, collaborators can perform a wide range of analytics without needing to code. Here are just a few of the many analytics dashboards you can access:

  • Visualizations: UMAP, t-SNE, violin plots, box plots, dot plots, heatmaps, correlation plots, and more

  • Differential expression & pathway enrichment

  • Marker gene analysis

  • Automatic cell type prediction

  • Sub-clustering

  • Trajectory analysis

  • Cell-cell communication

  • Cross-study and cross-omics summary




Access C-DIAM

The ability to collaborate efficiently on single-cell data analysis is critical. C-DIAM Multi-omics Studio helps streamline the sharing and exploration of Seurat and Scanpy objects, eliminating the traditional back-and-forth over static visuals. This allows your team to dive deep into the data and generate new insights faster.


Interested in giving it a try? Simply send us a request to access the platform. We’d be thrilled to support you as you explore the next frontier in multi-omics analysis!




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