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

作     者：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 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

作者机构：State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjing 211166China College of Biomedical Information and Engineeringthe First Affiliated Hospital of Hainan Medical UniversityHainan Medical UniversityHaikou 571199HainanChina College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin 150081HeilongjiangChina Department of ImmunologyNanjing Medical UniversityNanjing 211166China Department of Laboratory MedicineWomen and Children’s Hospital of Chongqing Medical UniversityChongqing 401174China Baylor College of MedicineHoustonTX 77030USA Shenzhen Institute for Advanced StudyUniversity of Electronic Science and Technology of ChinaShenzhen 518110GuangdongChina School of Biomedical Sciences and PharmacyFaculty of Health and Medicinethe University of NewcastleUniversity DriveCallaghanNSW 2308Australia Precision Medicine Research ProgramHunter Medical Research InstituteNew Lambton HeightsNSW 2305Australia 

出 版 物：《Military Medical Research》 (军事医学研究（英文版）)

年 卷 期：2023年第10卷第4期

页      面：529-553页

核心收录：

学科分类：0710[理学-生物学] 071010[理学-生物化学与分子生物学] 081704[工学-应用化学] 1001[医学-基础医学(可授医学、理学学位)] 07[理学] 08[工学] 0817[工学-化学工程与技术] 10[医学] 

基　　金：suppor ted by 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) 

主　　题：Single-cell RNA-sequencing(scRNA-seq) Data analysis Biomedical research Clinical applications 

摘      要：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 *** 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 ***,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 *** summarizing the current methods for each analysis step,we also provide an online repository of software and wrapped-up scripts to support the *** and caveats are pointed out for some specific analysis tasks and *** hope this resource will be helpful to researchers engaging with scRNA-seq,in particular for emerging clinical applications.