SAVER: Gene expression recovery for single-cell RNA sequencing

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 lowly and moderately expressed genes which hinders downstream analysis. To address this challenge, we introduce SAVER (Single-cel...

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Detalles Bibliográficos
Autores principales: Huang, Mo, Wang, Jingshu, Torre, Eduardo, Dueck, Hannah, Shaffer, Sydney, Bonasio, Roberto, Murray, John I., Raj, Arjun, Li, Mingyao, Zhang, Nancy R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2018
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030502/
https://www.ncbi.nlm.nih.gov/pubmed/29941873
http://dx.doi.org/10.1038/s41592-018-0033-z
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author Huang, Mo
Wang, Jingshu
Torre, Eduardo
Dueck, Hannah
Shaffer, Sydney
Bonasio, Roberto
Murray, John I.
Raj, Arjun
Li, Mingyao
Zhang, Nancy R.
author_facet Huang, Mo
Wang, Jingshu
Torre, Eduardo
Dueck, Hannah
Shaffer, Sydney
Bonasio, Roberto
Murray, John I.
Raj, Arjun
Li, Mingyao
Zhang, Nancy R.
author_sort Huang, Mo
collection PubMed
description 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 lowly and moderately expressed genes which hinders downstream analysis. To address this challenge, we introduce SAVER (Single-cell Analysis Via Expression Recovery), an expression recovery method for UMI-based scRNA-seq data that borrows information across genes and cells to obtain accurate expression estimates for all genes.
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spelling pubmed-60305022018-12-25 SAVER: Gene expression recovery for single-cell RNA sequencing Huang, Mo Wang, Jingshu Torre, Eduardo Dueck, Hannah Shaffer, Sydney Bonasio, Roberto Murray, John I. Raj, Arjun Li, Mingyao Zhang, Nancy R. Nat Methods Article 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 lowly and moderately expressed genes which hinders downstream analysis. To address this challenge, we introduce SAVER (Single-cell Analysis Via Expression Recovery), an expression recovery method for UMI-based scRNA-seq data that borrows information across genes and cells to obtain accurate expression estimates for all genes. 2018-06-25 2018-07 /pmc/articles/PMC6030502/ /pubmed/29941873 http://dx.doi.org/10.1038/s41592-018-0033-z Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Huang, Mo
Wang, Jingshu
Torre, Eduardo
Dueck, Hannah
Shaffer, Sydney
Bonasio, Roberto
Murray, John I.
Raj, Arjun
Li, Mingyao
Zhang, Nancy R.
SAVER: Gene expression recovery for single-cell RNA sequencing
title SAVER: Gene expression recovery for single-cell RNA sequencing
title_full SAVER: Gene expression recovery for single-cell RNA sequencing
title_fullStr SAVER: Gene expression recovery for single-cell RNA sequencing
title_full_unstemmed SAVER: Gene expression recovery for single-cell RNA sequencing
title_short SAVER: Gene expression recovery for single-cell RNA sequencing
title_sort saver: gene expression recovery for single-cell rna sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030502/
https://www.ncbi.nlm.nih.gov/pubmed/29941873
http://dx.doi.org/10.1038/s41592-018-0033-z
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