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

Min SuTao PanQiu-Zhen ChenWei-Wei ZhouYi GongGang XuHuan-Yu YanSi LiQiao-Zhen ShiYa ZhangXiao HeChun-Jie JiangShi-Cai FanXia LiMurray J CairnsXi WangYong-Sheng Li
Published in: Military Medical Research (2022)
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.
Keyphrases
  • data analysis
  • single cell
  • rna seq
  • high throughput
  • quality control
  • electronic health record
  • healthcare
  • primary care
  • clinical practice
  • working memory
  • deep learning