TrailmakerTM now has the option to run downstream data analysis in either Seurat or in Scanpy. The new Scanpy functionality is currently in beta mode, and your feedback will help us make it even better for you!
Why test Scanpy beta mode in Trailmaker
The main reason we’re adding the Scanpy option to the Insights module is to enable the analysis and visualization of multi-million cell datasets. We all know that single cell RNA-seq projects are getting bigger - as demonstrated by Parse Biosciences’ recent launch of the 5M cell EvercodeTM WT Penta kit - and we want Trailmaker to continue to provide a user-friendly solution for data analysis. The added benefit for all users, even if you have a smaller dataset of less than a million cells, is that Scanpy will offer a faster alternative method of analysis.
If you’re currently analyzing Parse Evercode WT Mega data, we recommend that you access Trailmaker using Scanpy beta mode. In the future, when this feature is fully launched, Scanpy will be the default method of analysis for Mega kit data.
How to access Scanpy beta mode in Trailmaker
Access or sign up to Trailmaker via this link:
https://app.trailmaker.parsebiosciences.com/
Since the new Scanpy option is currently in beta mode and doesn’t have full functionality yet (see details below), we recommend that you copy an existing project in your account using the Copy button:
Alternatively, you can grab a project from the dataset repository to test the Scanpy beta mode functionality:
Within your selected project, navigate to the Data Integration step (step 6) of Data Processing. Select the Scanpy option, and click apply to apply the Scanpy beta mode settings to your project. Note that Harmony is currently the only integration method available in Scanpy beta mode.
When data processing completes, your project will be ready to explore in Scanpy beta mode!
Feature availability in Scanpy beta mode
When using Scanpy beta mode, Harmony is the only integration method available. This method is equivalent to the Harmony method that is available for Seurat analyses. We plan to implement additional integration methods in Scanpy in the future.
When navigating through the Data Exploration and Plots & Tables pages in Scanpy beta mode, you might notice that some features are disabled and have a message “This feature is available for Seurat projects but is not yet implemented in Scanpy beta mode - it's coming soon!”
Your feedback on which of these features that are not yet available are most essential to your analysis will help us to prioritize implementation.
How to provide feedback
We’d love to hear your feedback on your experience with testing Scanpy beta mode. Your feedback will help us to understand and prioritize the aspects of this feature which require further improvements prior to full release. Whether that is adding additional features that are not yet available in Scanpy beta mode, or improving the performance of existing features. The more detailed feedback you can provide, the better we will understand your needs.
To provide feedback, click on the ‘Support’ button on the left navigation bar, and start your message with “Scanpy beta mode feedback”.
We’d like to take this opportunity to thank you for testing the Trailmaker’s new Scanpy beta mode!