Comparing single-cell RNA integration methods | Which is the best?

Which single-cell integration method is the best? In this video I compare 5 different methods using 3 different challenging integration problems. I test Seurat CCA, Seurat RPCA, SCVI-tools, and Scanorama. I measure time and memory usage and also examine integration outcomes. Github: https://github.com/mousepixels/sanbomics_scripts/tree/main/integration_comparison Datasets: https://www.cell.com/cell/fulltext/S0092-8674(19)30039-X https://www.nature.com/articles/s41591-021-01329-2 muscle/lung: unpublished