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Nat Methods. 2018 Jul;15(7):539-542. doi: 10.1038/s41592-018-0033-z. Epub 2018 Jun 25.

SAVER: gene expression recovery for single-cell RNA sequencing.

Author information

1
Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA.
2
Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
3
Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
4
Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
5
Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
6
Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
7
Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA. nzh@wharton.upenn.edu.

Abstract

In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable quantification of genes with low or moderate expression, which hinders downstream analysis. To address this challenge, we developed SAVER (single-cell analysis via expression recovery), an expression recovery method for unique molecule index (UMI)-based scRNA-seq data that borrows information across genes and cells to provide accurate expression estimates for all genes.

PMID:
29941873
PMCID:
PMC6030502
DOI:
10.1038/s41592-018-0033-z
[Indexed for MEDLINE]
Free PMC Article

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