Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
European Bioinformatics Institute · Centre for Human Genetics · +4 more institutions
Abstract
Motivation: 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. Results: We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for…
Citation impact
- FWCI
- 53.96
- Percentile
- 100%
- References
- 63
Authors
4- DJDavis J. McCarthyCorresponding
European Bioinformatics Institute, Centre for Human Genetics, University of Oxford, St Vincents Institute of Medical Research
- KRKieran R. Campbell
Centre for Human Genetics, University of Oxford
- ATAaron T. L. Lun
University of Cambridge
- QFQuin F. Wills
Centre for Human Genetics, John Radcliffe Hospital, University of Oxford
Topics & keywords
- Normalization (sociology)
- Visualization
- Computer science
- RNA-Seq
- Software
- Computational biology
- Data mining
- Biology
- Industry, innovation and infrastructure