README.md

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

CellSIUS: Cell Subtype Identification from Upregulated gene Sets

CellSIUS is an R package enabling 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.

Reference

Wegmann et Al., CellSIUS provides sensitive and specific detection of rare cell populations from complex single cell RNA-seq data, Genome Biology, 2019 [accepted]

Novartis/CellSIUS documentation built on June 4, 2019, 12:01 a.m.