Novartis/CellSIUS: CellSIUS: Cell Subtype Identification from Upregulated gene Sets

CellSIUS enables the identification and characterization of (rare) cell sub-populations from complex scRNA-seq datasets: it takes as input expression values of N cells grouped into M(>1) clusters. Within each cluster, genes with a bimodal distribution are selected and only genes with cluster-specific expression are retained. Among these candidate marker genes, sets with correlated expression patterns are identified by graph-based clustering. Finally, cells are assigned to subgroups based on their average expression of each gene set. The CellSIUS algorithm output provides the rare/ sub cell types by cell indices and their transcriptomic signatures.

install.packages("remotes")
remotes::install_github("Novartis/CellSIUS")