title: 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, 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 downstream analysis. scater provides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development.
  
  
  
  The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater .
  
  
  
  davis@ebi.ac.uk.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.|St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.
authors.forename: Davis J
authors.initials: DJ
authors.lastname: McCarthy
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.|Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK.
authors.forename: Kieran R
authors.initials: KR
authors.lastname: Campbell
authors.affiliation: CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
authors.forename: Aaron T L
authors.initials: AT
authors.lastname: Lun
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.|Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
authors.forename: Quin F
authors.initials: QF
authors.lastname: Wills
mesh_terms: D002460:Cell Line; D006801:Humans; D025341:Principal Component Analysis; D011381:Programming Languages; D011786:Quality Control; D012313:RNA / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods* / Q000592:standards*; D059010:Single-Cell Analysis / Q000379:methods*; D012984:Software; D013223:Statistics as Topic
chemical_list: D012313:RNA