Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF

We describe a new iteration of ICGS that outperforms state-of-the-art scRNA-Seq detection workflows when applied to well-established benchmarks. This approach combines multiple complementary subtype detection methods (HOPACH, sparse-NMF, cluster "fitness", SVM) to resolve rare and common cell-states, while minimizing differences due to donor or batch effects. Using data from multiple cell atlases, we show that the PageRank algorithm effectively down-samples ultra-large scRNA-Seq datasets, without losing extremely rare or transcriptionally similar yet distinct cell-types and while recovering novel transcriptionally distinct cell populations. We believe this new approach holds tremendous promise in reproducibly resolving hidden cell populations in complex datasets.