Volume 8 Issue 3
Jun.  2022
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Jiangping He, Lihui Lin, Jiekai Chen. Practical bioinformatics pipelines for single-cell RNA-seq data analysis[J]. Biophysics Reports, 2022, 8(3): 158-169. doi: 10.52601/bpr.2022.210041
Citation: Jiangping He, Lihui Lin, Jiekai Chen. Practical bioinformatics pipelines for single-cell RNA-seq data analysis[J]. Biophysics Reports, 2022, 8(3): 158-169. doi: 10.52601/bpr.2022.210041

Practical bioinformatics pipelines for single-cell RNA-seq data analysis

doi: 10.52601/bpr.2022.210041
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  • Corresponding author: chen_jiekai@gibh.ac.cn (J. Chen)
  • Received Date: 19 August 2021
  • Accepted Date: 01 March 2022
  • Available Online: 25 July 2022
  • Publish Date: 22 June 2022
  • Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool to explore cells. With an increasing number of scRNA-seq data analysis tools that have been developed, it is challenging for users to choose and compare their performance. Here, we present an overview of the workflow for computational analysis of scRNA-seq data. We detail the steps of a typical scRNA-seq analysis, including experimental design, pre-processing and quality control, feature selection, dimensionality reduction, cell clustering and annotation, and downstream analysis including batch correction, trajectory inference and cell–cell communication. We provide guidelines according to our best practice. This review will be helpful for the experimentalists interested in analyzing their data, and will aid the users seeking to update their analysis pipelines.

  • Jiangping He, Lihui Lin and Jiekai Chen declare that they have no conflict of interest.
    This article does not contain any studies with human or animal subjects performed by any of the authors

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