From 08348dc8d808e30a4f7c174cc4b5304ac2dcfdd6 Mon Sep 17 00:00:00 2001 From: "marilisa.neri@novartis.com" Date: Thu, 30 May 2019 11:35:40 +0200 Subject: [PATCH] first commit --- README.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..c046a88 --- /dev/null +++ b/README.md @@ -0,0 +1,15 @@ +# 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] +