Compare clusters from different datasets
I've been working with the multi-CCA alignment workflow in the Seurat package and am very impressed with functionality. As usual, the CCA tutorial is excellent for an alignment workflow and will get you off the ground quickly. You can even use the DESeq2 algorithm for determining differential expression from within Seurat.

When you use the function RunCCA() you can pass rescale.groups=TRUE if you wish to re-scale.

Abstracted workflow


Data preprocessing and gene selection
Define a shared correlation space with canonical correlation analysis
Remove dataset specific cells
Align correlated subspaces using dynamic time warping
Integrated analysis across datasets (clustering, trajectory building, etc ...)




Butler, A., and Satija, R. (2017). Integrated analysis of single cell transcriptomic data across conditions, technologies, and species.