8. Integration

For the integration part of this practical, we are going to follow the Seurat Introduction to scRNA-seq integration vignette.

Perform analysis without integration

With your knowledge of scRNASeq data analysis which step of this analysis could you improve ?

Perform integration

In their paper Korsunsky, Millard et al. 2019 present a method to integrate different single-cell NGS dataset.

Check the Figure 1 of the paper to understand the principles of the harmony algorithm.

How is it different from SCTransform ?

Use the Harmony algorithm for the integration

Identify conserved cell type markers & Identify differential expressed genes across conditions

From a statistical point of view, what can you say about these testing procedures ?

Data integration can also be used to analyse scRNASeq data with spacial scRNASeq data