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Frequently Asked Questions

In our most recent release, we’ve added new methods, and significantly restructured and improved our codebase. We outline the most significant changes below, particularly for users who have extensive experience with Seurat or want to learn more about the details of the Seurat object.

For new users, especially those getting started with analyzing scRNA-seq data, we suggest working through our guided tutorial of a 2,700 PBMC scRNA-seq dataset from 10X genomics. If you use Seurat v2.0 or above in your research, please considering citing Butler et al., Nature Biotechnology 2018.

1. What new methods are included in Seurat v2.0?

2. Why did function and slot names change in v2.0?

3. Can I use my old Seurat object (from v1.4 or below) in v2.0?

4. How can I find out about more about additional features?

5. How do I select which PCs to use for clustering?

6. How do I select my set of variable genes?

7. How is data stored within the Seurat object? What is the difference between raw.data, data, and scale.data?

8. Any new features coming soon?