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Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

Abstract:

Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization.We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, qual...

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Publication status:
Published
Peer review status:
Peer reviewed
Version:
Publisher's version

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Publisher copy:
10.1093/bioinformatics/btw777

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Institution:
University of Oxford
Division:
Medical Sciences Division
Department:
NDM; Human Genetics Wt Centre
Role:
Author
ORCID:
0000-0002-2218-6833
More by this author
Institution:
University of Oxford
Division:
Medical Sciences Division
Department:
NDM; Human Genetics Wt Centre
Role:
Author
More by this author
Institution:
University of Oxford
Division:
Medical Sciences Division
Department:
RDM; Weatherall Insti. for Molecular Medicine
Role:
Author
Publisher:
Oxford University Press Publisher's website
Journal:
Bioinformatics Journal website
Volume:
33
Issue:
8
Pages:
1179-1186
Publication date:
2017-01-14
Acceptance date:
2016-12-07
DOI:
EISSN:
1367-4811
ISSN:
1367-4803
Pubs id:
pubs:673358
URN:
uri:d5c7de0c-3a03-4874-81a5-e555d3ef1282
UUID:
uuid:d5c7de0c-3a03-4874-81a5-e555d3ef1282
Local pid:
pubs:673358
Paper number:
8

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