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CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data.

ABSTRACT: 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.

SUBMITTER: Wegmann R

PROVIDER: S-EPMC6637521 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data.

Wegmann Rebekka R Neri Marilisa M Schuierer Sven S Bilican Bilada B Hartkopf Huyen H Nigsch Florian F Mapa Felipa F Waldt Annick A Cuttat Rachel R Salick Max R MR Raymond Joe J Kaykas Ajamete A Roma Guglielmo G Keller Caroline Gubser CG

Genome biology 20190717 1

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 compl ...[more]

PMID: 31315641

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