propeller: testing for differences in cell type proportions in single cell data

Belinda Phipson; Choon Boon Sim; Enzo R Porrello; Alex W Hewitt; Joseph Powell; Alicia Oshlack

Journal article

propeller: testing for differences in cell type proportions in single cell data

Belinda Phipson, Choon Boon Sim, Enzo R Porrello, Alex W Hewitt, Joseph Powell, Alicia Oshlack

BIOINFORMATICS | OXFORD UNIV PRESS | Published : 2022

DOI: 10.1093/bioinformatics/btac582

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Abstract

Single cell RNA-Sequencing (scRNA-seq) has rapidly gained popularity over the last few years for profiling the transcriptomes of thousands to millions of single cells. This technology is now being used to analyse experiments with complex designs including biological replication. One question that can be asked from single cell experiments, which has been difficult to directly address with bulk RNA-seq data, is whether the cell type proportions are different between two or more experimental conditions. As well as gene expression changes, the relative depletion or enrichment of a particular cell type can be the functional consequence of disease or treatment. However, cell type proportion estima..

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University of Melbourne Researchers

Belinda Phipson Author

Enzo Porrello Author

Alicia Oshlack Author

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Grants

Awarded by National Health and Medical Research Council

Awarded by Novo Nordisk Foundation

Funding Acknowledgements

This work was supported by a National Health and Medical Research Council Investigator grant [GNT1175653 to B.P.]; a National Health and Medical Research Council Investigator grant [GNT1196256 to A.O.]; a National Health and Medical Research Council Investigator grant [GNT1175781 to J.P.]; and a National Health and Medical Research Council Investigator grant [GNT2008376 to E.R.P.]. The work was supported by National Health and Medical Research Council Grant [GNT1187748]. The snRNA-seq dataset for heart was funded by Royal Children's Hospital Foundation and National Health and Medical Research Council Project grant [GNT1160257]. The Novo Nordisk Foundation Center for Stem Cell Medicine is supported by Novo Nordisk Foundation grants [NNF21CC0073729 to E.R.P.]. MCRI is supported by the Victorian Government's Operational Infrastructure Support Program.