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

Bioinformatics. 2017 Apr 15;33(8):1179-1186. doi: 10.1093/bioinformatics/btw777.


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 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.

Availability and implementation: The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at .


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Cell Line
  • Humans
  • Principal Component Analysis
  • Programming Languages*
  • Quality Control
  • RNA / genetics
  • Sequence Analysis, RNA / methods*
  • Sequence Analysis, RNA / standards*
  • Single-Cell Analysis / methods*
  • Software*
  • Statistics as Topic


  • RNA