https://github.com/novartis/cellsius

CellSIUS: Cell Subtype Identification from Upregulated gene Sets
https://github.com/novartis/cellsius

Last synced: 11 months ago
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CellSIUS: Cell Subtype Identification from Upregulated gene Sets

• Host: GitHub
• URL: https://github.com/novartis/cellsius
• Owner: Novartis
• License: apache-2.0
• Created: 2019-05-30T09:33:37.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2019-06-03T15:13:42.000Z (about 7 years ago)
• Last Synced: 2024-04-16T11:10:09.102Z (about 2 years ago)
• Language: R
• Size: 11 MB
• Stars: 5
• Watchers: 24
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

          
# 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.

[![DOI](https://zenodo.org/badge/189385961.svg)](https://zenodo.org/badge/latestdoi/189385961)

## 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]