Seurat Single Cell Analysis Tool Kit Version 5

A workaround to use Seurat v5 with other R/python packages

With the release of version 5 of seurat, one of the major changes that has been pushed is its new data-structure.

Surat v5 data-structure is drastically different from its previous versions and because of this running tools that require alternative data structures that stores your single cell assays still remains a challenge; most of the conversion functions expects older seurat objects like data-structures.

In this post, i will share my workaround that allows me to use the new features of Seurat v5 such as pseudo-bulk analysis while still allowing me to use other packages that i require in my analysis workflow.

One of the common alternative data-structures that is widely used to store single cell assays is known as the `SingleCellExperiment` class, and if you are using packages other than seurat, you may need to switch or transform your seurat object assay class to `SingleCellExperiment` class.

For Example: when running doublet finder packages or integration using methods that are not currently supported within the seurat framework, you may need to convert your seurat objects to SingleCellExperiment class first.