Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

Nat Protoc. 2021 Jan;16(1):1-9. doi: 10.1038/s41596-020-00409-w. Epub 2020 Dec 7.


Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows you to profile the whole transcriptome of a large number of individual cells. However, the analysis of the large volumes of data generated from these experiments requires specialized statistical and computational methods. Here we present an overview of the computational workflow involved in processing scRNA-seq data. We discuss some of the most common tasks and the tools available for addressing central biological questions. In this article and our companion website ( https://scrnaseq-course.cog.sanger.ac.uk/website/index.html ), we provide guidelines regarding best practices for performing computational analyses. This tutorial provides a hands-on guide for experimentalists interested in analyzing their data as well as an overview for bioinformaticians seeking to develop new computational methods.

Publication types

  • Review

MeSH terms

  • Animals
  • Gene Expression Profiling / methods
  • Genomics / methods
  • Humans
  • RNA / genetics
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*
  • Software
  • Transcriptome
  • Workflow


  • RNA