scRNA-seq data analysis method to improve analysis performance

IF 3.8 4区工程技术 Q1 BIOCHEMICAL RESEARCH METHODS

IET nanobiotechnology Pub Date : 2023-02-02 DOI:10.1049/nbt2.12115

Junru Lu, Yuqi Sheng, Weiheng Qian, Min Pan, Xiangwei Zhao, Qinyu Ge

引用次数: 1

Abstract

With the development of single-cell RNA sequencing technology (scRNA-seq), we have the ability to study biological questions at the level of the individual cell transcriptome. Nowadays, many analysis tools, specifically suitable for single-cell RNA sequencing data, have been developed. In this review, the currently commonly used scRNA-seq protocols are discussed. The upstream processing flow pipeline of scRNA-seq data, including goals and popular tools for reads mapping and expression quantification, quality control, normalization, imputation, and batch effect removal is also introduced. Finally, methods to evaluate these tools in both cellular and genetic dimensions, clustering and differential expression analysis are presented.

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scRNA-seq数据分析方法，提高分析性能

随着单细胞RNA测序技术(scRNA-seq)的发展，我们有能力在单个细胞转录组水平上研究生物学问题。目前，已经开发出许多专门适用于单细胞RNA测序数据的分析工具。本文对目前常用的scRNA-seq协议进行了综述。本文还介绍了scRNA-seq数据的上游处理流程，包括目标和常用的reads映射和表达量化、质量控制、归一化、imputation和批次效应去除的工具。最后，介绍了在细胞和遗传维度、聚类和差异表达分析方面评估这些工具的方法。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

IET nanobiotechnology 工程技术-纳米科技

CiteScore

6.20

自引率

4.30%

发文量

审稿时长

1 months

期刊介绍： Electrical and electronic engineers have a long and illustrious history of contributing new theories and technologies to the biomedical sciences. This includes the cable theory for understanding the transmission of electrical signals in nerve axons and muscle fibres; dielectric techniques that advanced the understanding of cell membrane structures and membrane ion channels; electron and atomic force microscopy for investigating cells at the molecular level. Other engineering disciplines, along with contributions from the biological, chemical, materials and physical sciences, continue to provide groundbreaking contributions to this subject at the molecular and submolecular level. Our subject now extends from single molecule measurements using scanning probe techniques, through to interactions between cells and microstructures, micro- and nano-fluidics, and aspects of lab-on-chip technologies. The primary aim of IET Nanobiotechnology is to provide a vital resource for academic and industrial researchers operating in this exciting cross-disciplinary activity. We can only achieve this by publishing cutting edge research papers and expert review articles from the international engineering and scientific community. To attract such contributions we will exercise a commitment to our authors by ensuring that their manuscripts receive rapid constructive peer opinions and feedback across interdisciplinary boundaries. IET Nanobiotechnology covers all aspects of research and emerging technologies including, but not limited to: Fundamental theories and concepts applied to biomedical-related devices and methods at the micro- and nano-scale (including methods that employ electrokinetic, electrohydrodynamic, and optical trapping techniques) Micromachining and microfabrication tools and techniques applied to the top-down approach to nanobiotechnology Nanomachining and nanofabrication tools and techniques directed towards biomedical and biotechnological applications (e.g. applications of atomic force microscopy, scanning probe microscopy and related tools) Colloid chemistry applied to nanobiotechnology (e.g. cosmetics, suntan lotions, bio-active nanoparticles) Biosynthesis (also known as green synthesis) of nanoparticles; to be considered for publication, research papers in this area must be directed principally towards biomedical research and especially if they encompass in vivo models or proofs of concept. We welcome papers that are application-orientated or offer new concepts of substantial biomedical importance Techniques for probing cell physiology, cell adhesion sites and cell-cell communication Molecular self-assembly, including concepts of supramolecular chemistry, molecular recognition, and DNA nanotechnology Societal issues such as health and the environment Special issues. Call for papers: Smart Nanobiosensors for Next-generation Biomedical Applications - https://digital-library.theiet.org/files/IET_NBT_CFP_SNNBA.pdf Selected extended papers from the International conference of the 19th Asian BioCeramic Symposium - https://digital-library.theiet.org/files/IET_NBT_CFP_ABS.pdf