Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications

Min Su; Tao Pan; Qiu-Zhen Chen; Wei-Wei Zhou; Yi Gong; Gang Xu; Huan-Yu Yan; Si Li; Qiao-Zhen Shi; Ya Zhang; Xiao He; Chun-Jie Jiang; Shi-Cai Fan; Xia Li; Murray J. Cairns; Xi Wang; Yong-Sheng Li

doi:10.1186/s40779-022-00434-8

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Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications

REVIEW | Updated：2023-09-05

- Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications
- Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications
- MMR 2023年10卷第4期页码：529-553
- Affiliations：
  
  1.State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
  2.College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou 571199, China
  3.College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
  4.Department of Immunology, Nanjing Medical University, Nanjing 211166, China
  5.Department of Laboratory Medicine, Women and Children’s Hospital of Chongqing Medical University, Chongqing 401174, China
  6.Baylor College of Medicine, Houston, TX 77030, USA
  7.Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China, Shenzhen 518110, Guangdong, China
  8.School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, the University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
  9.Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
- Author bio：
  
  * lixia@hrbmu.edu.cn;
  murray.cairns@newcastle.edu.au;
  xiwang@njmu.edu.cn;
  liyongsheng@hainmc.edu.cn
- Funds：
  
  the National Key Research and Development Program of China(2022YFC2702502);the National Natural Science Foundation of China(32170742;31970646;and 32060152);the Start Fund for Specially Appointed Professor of Jiangsu Province, Hainan Province Science and Technology Special Fund(ZDYF2021SHFZ051);the Natural Science Foundation of Hainan Province(820MS053);the Start Fund for High-level Talents of Nanjing Medical University(NMUR2020009);the Marshal Initiative Funding of Hainan Medical University(JBGS202103);the Hainan Province Clinical Medical Center(QWYH202175);the Bioinformatics for Major Diseases Science Innovation Group of Hainan Medical University;the Shenzhen Science and Technology Program(JCYJ20210324140407021)
- DOI：10.1186/s40779-022-00434-8
  中图分类号：
- 纸质出版：2023-08
- Accepted：
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Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications[J]. MMR, 2023,10(4):529-553.

Su M, Pan T, Chen QZ, Zhou WW, Gong Y, Xu G, et al. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res. 2022;9(1):68.
Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications[J]. MMR, 2023,10(4):529-553. DOI： 10.1186/s40779-022-00434-8.

Su M, Pan T, Chen QZ, Zhou WW, Gong Y, Xu G, et al. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res. 2022;9(1):68. DOI： 10.1186/s40779-022-00434-8.

摘要

Abstract

The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity for high-throughput scRNA-seq

including clinical samples

the analysis of these huge volumes of data has become a daunting prospect for researchers entering this field. Here

we review the workflow for typical scRNA-seq data analysis

covering raw data processing and quality control

basic data analysis applicable for almost all scRNA-seq data sets

and advanced data analysis that should be tailored to specific scientific questions. While summarizing the current methods for each analysis step

we also provide an online repository of software and wrapped-up scripts to support the implementation. Recommendations and caveats are pointed out for some specific analysis tasks and approaches. We hope this resource will be helpful to researchers engaging with scRNA-seq

in particular for emerging clinical applications.

关键词

Keywords

references

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