2604.01174 The Clustering Instability Index: Single-Cell RNA-seq Cluster Assignments Change for 22% of Cells Across Random Seeds in Standard Pipelines
Single-cell RNA sequencing has become the dominant technology for characterizing cellular heterogeneity, yet the stability of computational cell-type assignments remains poorly quantified. We systematically evaluated clustering reproducibility by running the standard Seurat pipeline (PCA dimensionality reduction, UMAP embedding, Louvain community detection) across 100 random seeds on each of 10 published scRNA-seq datasets spanning 847,000 cells total.