CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data.
Benchmarking
Choroid plexus
Clustering
Cortical development
Data analysis
Human pluripotent stem cells
Lineage mapping
Rare cell types
Single-cell RNA sequencing
Software
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
17 07 2019
17 07 2019
Historique:
received:
07
05
2019
accepted:
13
06
2019
entrez:
19
7
2019
pubmed:
19
7
2019
medline:
7
8
2019
Statut:
epublish
Résumé
We develop CellSIUS (Cell Subtype Identification from Upregulated gene Sets) to fill a methodology gap for rare cell population identification for scRNA-seq data. CellSIUS outperforms existing algorithms for specificity and selectivity for rare cell types and their transcriptomic signature identification in synthetic and complex biological data. Characterization of a human pluripotent cell differentiation protocol recapitulating deep-layer corticogenesis using CellSIUS reveals unrecognized complexity in human stem cell-derived cellular populations. CellSIUS enables identification of novel rare cell populations and their signature genes providing the means to study those populations in vitro in light of their role in health and disease.
Identifiants
pubmed: 31315641
doi: 10.1186/s13059-019-1739-7
pii: 10.1186/s13059-019-1739-7
pmc: PMC6637521
doi:
Types de publication
Evaluation Study
Journal Article
Langues
eng
Pagination
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