Comparison of Clusters/Cell Types Across Different Samples

[christos-efthymiou]

Hello, I am working with some 10x sequencing data and I have 5 samples with different conditions that I am comparing. I have started by creating Seurat objects for each sample, followed by the standard quality control and filtering steps I've seen in the Seurat vignettes. I then normalized and identified variable features for each dataset independently, selected features that are repeatedly variable across datasets for integration and ran PCA on each dataset using these features, and then ran integration and the standard visualization and clustering steps.

One piece of information that I am interested in is the comparison of clusters/cell types across my different samples. Specifically, I would like to be able to compare the sizes/proportions of each cluster across samples to determine if there are statistically significant differences, as well as determining if there are entirely new or different clusters in each sample. How would I go about comparing the clusters across samples to find unique ones in certain samples, as well as comparing similar samples for differences in size/proportion?