Topic
Overclustering
Are my clusters real cell types or artifacts of the resolution I picked?
Louvain and Leiden will split any point cloud into as many pieces as the resolution allows. A cluster is only real if it has markers you can name, holds up across samples, and is not explained by cell cycle, stress, doublets or sequencing depth.
- How to Tell If You Overclustered in Single-Cell ATAC-seq
Louvain and Leiden will keep splitting your point cloud for as long as you keep raising resolution, here's how to find out whether the clusters you kept are real.
- How to Tell If You Overclustered in Single-Cell RNA-seq
Louvain and Leiden will hand you as many clusters as your resolution allows; the only test that matters is whether each one has markers you can name and cells from more than one sample.
- How to Tell If You Overclustered in Single-Nucleus RNA-seq
Leiden will happily hand you fifty clusters from thirty cell types if the resolution lets it; the object itself can't tell you which cuts are real.
- How to Tell If You Overclustered in Spatial Transcriptomics
Leiden and Louvain will happily cut your tissue into as many pieces as the resolution allows; the algorithm has no opinion on whether any of those pieces is a real cell type.